I think they usually do get along, but their underlying issues are bound to reoccur at times, especially given how we know they don't actually interact as much as one might think outside of official work (what with Luna normally being asleep during the day, Celestia asleep at night). The fact is Celestia and Luna don't have much in common while at the same time they both have a lot of pride and strong personalities, and that combination means there is always going to be some degree of conflict in their relationship. The key is that they keep the conflict constructive and not let it undermine their love for each other as sisters.