Yes, it may seem chaotic for a while. And yes, it gets easier. Try to relax a little! It always takes time to settle into a new home. What I would advise is to just put things where they seem to make the most sense for now, then wait and see how well it works. Not what you want to hear I bet
But really, don't overthink it. Your instincts might seem odd if you attempt to rationalize them too much but if you just trust them you might end up surprised.
I've moved a lot and find it can take at least 6 months to get truly settled, especially when you go into a larger place than you are used to. The real trick is to watch for patterns, then make them work for you. Keep an eye out for which door gets used the most (your spot for coats/shoes/keys/etc.. needs to be near THIS door, which might not be the one with a closet near it). Do people keep opening the same wrong drawer in search of silverware? Move it there.
Also try to remember that it doesn't need to be perfect because no matter what, it will change over the years anyway. Tastes/jobs/hobbies/habits change, kids get older, and your home will adjust to reflect all that. Also, of course, it is much easier to get more done when the toddler gets older. I am shocked lately at how much I can get done with my 4 year old around.
Good luck and enjoy the new house!