(CNN) It's hard to imagine that a convicted child rapist would be allowed to lead a church from prison, but that's exactly what's going on with Warren Jeffs.

Jeffs leads a polygamist sect known as the Fundamentalist Church of Jesus Christ of Latter-day Saints. It gained worldwide attention in 2006 when authorities accused Jeffs of sexual offenses against girls he took as wives. At one point Jeffs disappeared, prompting the FBI to put him on its 10 Most Wanted Fugitives list until he was captured.

In 2008, authorities raided the church's sprawling Texas ranch. Police removed more than 460 children from the property, including mothers under 18 years old. Authorities seized and shut down the ranch last year

Eventually, Jeffs was convicted in 2011 of "sexual assault" and "aggravated sexual assault" of two girls ages 12 and 15. He was sentenced to life in prison plus 20 years.

The FLDS broke away from the mainstream Mormon church more than a century ago because its members refused to renounce polygamy.

The church allegedly exercises control over the adjacent towns of Colorado City, Arizona, and Hildale, Utah -- an area informally known as Short Creek. Other enclaves exist in Mancos, Colorado; Boise City, Oklahoma Custer County, South Dakota ; and a Canadian community known as Bountiful, British Columbia.

FLDS leaders seldom speak with the news media and did not respond to CNN's multiple requests for comment on this story.

So, what's the status of FLDS today? Several key issues continue to play a role in the church's future:

'Seed bearers' and ritualistic sex

Although day-to-day leadership of the church is run mostly by Jeff's brother, Lyle Jeffs, Warren Jeffs actively directs church matters from prison, said Sam Brower, a private investigator who's been closely following FLDS activities for 10 years.

Brower's New York Times best-selling book "Prophet's Prey" inspired a documentary of the same name , which debuted at this year's Sundance Film Festival. He played a key role in the FBI's investigation of Jeffs' and his eventual conviction.

First obtained by the Salt Lake Tribune , a child custody petition filed in a St. George, Utah, juvenile court by Lyle Jeffs' estranged wife Charlene Jeffs describes a group of followers called "seed bearers." "A seed bearer is an elect man of a worthy bloodline chosen by the Priesthood to impregnate the FLDS woman," according to Charlene Jeffs' petition. Under a new doctrine, "FLDS men are no longer permitted to have children with their multiple wives. That privilege belongs to the seed bearer alone," the petition said. "It is the husband's responsibility to hold the hands of their wives while the seed bearer 'spreads his seed.' In layman terms, the husband is required to sit in the room while the chosen seed bearer, or a couple of them, rape his wife or wives," according to the document.

Utah juvenile court records are not usually available to the public, so it's unknown if anyone filed documents disputing any details in Charlene Jeffs' petition, or the veracity of the petition's allegations. Lyle Jeffs eventually agreed to share custody of their two teen children with Charlene Jeffs -- the Salt Lake Tribune reported -- with the children living with their mother.

Brower said he was able to confirm similar reports of "seed bearers" through his own sources. "It's ritualistic procreation," Brower said, "performed on a ritualistic bed-slash-altar." As part of this new system, Warren Jeffs has withheld any relationships between husbands and wives, Brower said. Any touching between spouses outside rituals like these, even a simple handshake, can now be considered adultery in the church.

When asked about his sources for this information, Brower would only say he didn't want to violate confidences. "I'm 100% satisfied as a private investigator that it exists," he said.

There has been no response to CNN's multiple attempts to connect with an FLDS representative to get their side of the story.

A convicted child rapist still leads the church

In the midst of his legal troubles, Jeffs resigned as church president in 2007. He retook control of the church four years later, after followers said he appeared to get more access to phone calls outside prison.

Chris Wyler — a lifelong church member until his expulsion in 2012 -- told CNN that he witnessed instances when Jeffs was "patched in" by phone so he could speak with church leaders.

Also, members were instructed to pray for God to free Jeffs, whom they call "the Prophet."

"We were told to pray for our Prophet's deliverance," said Wyler, age 38. "It meant the Lord would deliver him however he'd be delivered. Even if somebody was commanded to go get him out."

Federal crackdown in full swing

All these years after Jeffs' arrest, the FLDS continues to be targeted by federal law enforcement officials.

Warren Jeffs' prison mug shot

Brower stopped short of saying the federal government is trying to take the church down. "But, when you start chipping away at them like that, that starts causing problems," he said.

Brower, who likens the FLDS network to a crime syndicate, isn't the first to make that comparison. Senate Minority Leader Harry Reid, D-Nevada, has described polygamous sects generally as "a form of organized crime" that goes largely unchecked by law enforcement . Brower said this wave of federal action simply reinforces that idea.

Town marshals committed various offenses, including "returning at least one underage bride to a home from which she had fled," according to the complaint. They failed to investigate crimes against non-FLDS members and refused to arrest FLDS individuals who committed crimes against nonmembers, the complaint said

The towns now face a federal trial, which is set for January

Allegations of illegal child labor

JUST WATCHED See CNN's exclusive 2012 report on FLDS child labor Replay More Videos ... MUST WATCH See CNN's exclusive 2012 report on FLDS child labor 05:25

Children who were put to work included at least 125 who were younger than 12, at least 50 between ages 12 and 13, and at least 25 between 14 and 15, according to the suit. All performed tasks during school hours such as mowing, pruning and bagging pecans, the suit said.

Wyler, the former FLDS member, said his two oldest children — both under age 16 — took part in a pecan harvest a few years ago -- working 12 or 13 hours a day for about four days. His feelings about the practice are "mixed," he said.

"I think it's cool that people could go and help," Wyler said. "But if they're turning a profit, then the kids should be paid. Also, they shouldn't be taken out of school for that."

$100 million church fund

Since the 1940s, the church has been depositing real estate assets into a religious charitable trust called the United Effort Plan, which is now estimated to be worth around $100 million. Utah took control of the trust in 2005 after authorities began investigating the church. Many of these homes are owned by the trust -- but are occupied by FLDS members.

FLDS funds itself through ownership of various businesses. The church's major sources of revenue come from huge farming operations and widespread manufacturing and construction companies, said Brower.

The FLDS also raises money through tithes — a practice where followers make mandatory donations of 10% of their income. Church members have been asked to give "consecrations" — special monthly donations, sometimes around $1,000, Wyler said.

It was a financial disagreement that led to Wyler's departure from the church three years ago. He said he was told to give all his "earthly possessions" to the church -- or face expulsion. "I had a concern with that."

Dwindling membership

The number of followers in the secretive church is impossible to know for sure. At its peak many years ago, total FLDS membership may have been as high as 15,000, Brower said, but by his educated guess the number now -- in the wake of Jeffs' imprisonment and the civil lawsuit -- is somewhere near 10,000.

Brower said several thousand have left the church or been expelled within the past few years.

FLDS members did not send their children to public schools, which may explain reports of skyrocketing enrollment in public schools. Enrollments have been rising, as more members are expelled or leave the church.

Some members have been leaving FLDS with the help of advocacy groups in the region, such as Holding Out Help. "I've served hundreds of people here," Holding Out Help's director Ruth Olson told CNN's Lisa Ling. "We try to establish ourselves here so they can feel safe."

Jeffs' fourth child, 31-year-old Becky Jeffs, recently left the church. She said she had suffered abuse at the hands of her father. "So many people in the FLDS said, 'Oh you have the neatest father in the world,'" Becky Jeffs told Ling. "Now I just think, 'If you only knew...'"

It's hard to offer the FLDS perspective on all the allegations. The church didn't respond to multiple requests by CNN to defend itself.

For the leaders, Brower said, "it's about sex, money and power. And that's what drives them. But they also convince themselves ... that there's some meaning to their madness."

He said many rank-and-file members desperately want to stay with the church and follow the religious traditions of their parents, grandparents and great-grandparents. "They want to believe that the horrible things that are happening to their church are just a test that's being placed on them."

As for Wyler, he expects the church to survive.

"There's always going to be people that believe in it," he said. "No matter what evidence is presented to them."