SANTA CLARA, Calif. -- In the opening days of the San Francisco 49ers' organized team activities, there have been occasional moments when quarterback Brian Hoyer has turned to ask coach Kyle Shanahan a question only to find he's talking to nobody.

Such is the acclimation period for a quarterback who once had Shanahan as his offensive coordinator and could consistently count on Shanahan attentively watching every snap. But now that Shanahan is embarking on his first head-coaching opportunity, his time has to be spent doing more than overseeing an offense and tutoring his quarterbacks.

"For me, he's calling the plays so it's pretty much the same, but there's periods where I look around and maybe I'm ready to ask him a question and maybe he's with the defense," Hoyer said. "I think that's obviously part of the responsibility of being a head coach."

Kyle Shanahan (right) wants to have a holistic view of his team and does not want to focus on just one component. AP Photo/Marcio Jose Sanchez

Suffice to say, it's been a much bigger adjustment for Shanahan than for Hoyer. Although the 49ers are deep into their offseason program, this week has offered the first chance for Shanahan to have his entire team on the practice field doing actual football activities. It's the closest thing to a regular-season practice the offseason can provide.

And it's left anyone searching for Shanahan on the practice field playing something akin to a football version of the "Where's Waldo?" books.

"It's been awkward for me sometimes where to go," Shanahan said, laughing. "I'm used to knowing exactly where to go and what to do, and I always did that from an offensive coordinator standpoint, which I still do a lot of those responsibilities. So at times, I feel most comfortable when I go to do that because that's something to do.

"But when I pass it over to some other guys and let them do it, I find myself walking around a lot and I'm not used to that. It feels awkward, but I don't think it's a bad thing. I think I should walk around and watch everyone and see it. I always see it on the tape, but that's later at night. You want players to know you're there and paying attention to everything, and I usually try to cover that in meetings the next day also."

During Tuesday's OTA session open to the media, Shanahan could be seen bouncing from group to group, spending a large chunk of the early part of practice with the defensive line and linebackers as they went through "run fits." Even during team drills, Shanahan offered advice and tips to multiple position groups. In the next few weeks, it's safe to expect Shanahan to find a rhythm and figure out where he wants to be and when.

Much of that rhythm will come from what Shanahan sees on film when he goes back and watches each practice. Shanahan has already built a reputation among his players as the kind of detail-oriented coach who grinds through every second of the tape and has suggestions for players at every position in all three phases.

"He figures it out really quick," center Daniel Kilgore said. "As a head coach, he stands up there and watches film and breaks down everything: offense, defense, special teams. Not many head coaches in the league can probably do that. And he tells you why certain guys are in certain positions and why they're successful or what makes this play successful on the defensive side as well as the offensive side. He's super-intelligent, and the more and more comfortable he gets, it's going to be a bright future for him."

Since joining the 49ers in February, Shanahan has had the opportunity to interact with his team plenty, which is why he's still getting the hang of where to go on the practice field. It's the one place he hasn't been able to get into a routine yet. Kilgore said Shanahan seemed a bit nervous his first time speaking to the entire team, but has already noticed Shanahan getting more comfortable in his interactions with the full roster.

Beyond that, Shanahan has earned respect for how he's handled some potentially difficult situations. Shanahan and general manager John Lynch took the time to call linebacker NaVorro Bowman and tight end Vance McDonald when rumors of a potential trade swirled around them. McDonald, in particular, was surprised that his new coach, who had no previous relationship with him, would call to explain the situation after spending the previous few days holed up in the draft room.

"He's been in a draft room for 48 hours at that point, so I'm sure he's worn out, and he's calling me on his way home," McDonald said. "And the first thing I told him is, ‘Man, there's not a lot of coaches that would do this. So I'm sure you're worn out.' We were kind of joking. He just wanted to fill me in."

Armed with a six-year contract, Shanahan has plenty of time to get his bearings as a head coach, and that will come soon enough with more time on the practice field. While there might be some hiccups in the early going as Shanahan finds himself in charge of more than just the offense for the first time, he has no plans to go back to working with just one unit anytime soon.

"I think the main thing is I'll never just do one," Shanahan said. "I hope the rest of my career I'm doing a little bit of everything, and wherever you think you're needed the most, you work in that area and you focus on that and have confidence in everyone else to take care of the rest of the stuff. But you can't be everywhere. So you like to feel you can be where you're needed the most."

Exactly where that is, much like the 49ers as a team, is a work in progress.