It's a puzzle, that's all. There are multiple pieces, and your job is to put the pieces together--but this puzzle can be put together in different ways. There will be times where you find that you could have done things differently to maximize results, but you do your best and that's all you can do. As long as you keep the process moving forward at a proper speed, you're doing it right. If you're keeping things moving even better than that, you've REALLY got the hang of it. Along the way, you'll find secrets, like "oh, I know I can always put these two actors in the other room to work on X while we're rehearsing Y in this room." Then you'll always know to do that whenever Y is happening onstage.
The way I like to do it is to first put down the ideal schedule for the main rehearsal (i.e. the rehearsal the director is in), then the second priority (as long as no costume fittings, voice/text sessions, etc) is the rehearsal with the Asst. director, then the third with etc. etc. Fill out the perfect day's schedule for the main rehearsal. With that, then what can you do in the next room? Now once that's done, what can you do in the next room? There are multiple combinations for each day and you should try a few before setting the schedule.
it will work out. it will take time. it will get easier.