Hi J.,
First of all, THANK YOU to your husband for his service and to you for your support of your husband!
I can relate to your issue because as a stay at home mom, I spend more time w/ our 4 yr old and 1 yr old than my husband does, and have established the routine. What I can share is that while routines are good - regular mealtimes, regular naptimes - the WAY of doing things, or the process, doesn't need to be identical between you and your husband. You may have a certain way of giving your son a bath, or a process in the morning of getting him dressed. Your husband may have a different process for those tasks, but the end result is the same! Your little munchkin eventually gets clean, eventually gets dressed, etc.
I had a hard time letting go with our first born, because I figured the best way was my way. My husband finally said,"You make me feel like I can't do anything right, because you are always correcting me." After hearing that, it made me realize that my way is not the only way of doing things.
Also, lots of communication!! Let your husband know: this is what time junior usually wakes up, what time he eats, naps, etc. Then stand back and let your husband decide HOW he wants to get the things done. It might be hard, but there may be times you have to consciously work on not saying anything!
Basically, my suggestion would be as long as the end result is the same, try not to sweat how it gets done. I can only imagine how excited your husband is to be re-introduced to his son and to begin developing a relationship with him! Good luck!
M.