honestly, i am far more scheduled when dh is deployed simply because there are less out of the house activities to work around. he's very outgoing and i'm more of a homebody. bedtime routine is sacrosanct, and i try to have dinner ready about the same time every night, but i have found that a good schedule can be the enemy of a good connection when we are dealing with him being gone. when he is home he often works weird shifts, which also throws the schedule out the window. i could either be adamant about a routine, at the cost of natural, spontaneous connection and conversation, or i can just go with what works at that particular time on that particular day.
since your dh likes a schedule, maybe you could talk about what routine elements are really important to his sense of well being and calm and which are negotiable. maybe he has to have dinner ready at a certain time to feel like he can relax, but some other area can be let go a bit?
as far as communication, skype is awesome when my dh is in a port (he's in the navy), but usually we only have email. so we make an effort to have meaningful talks even though they aren't in the format we'd choose. when i email i give him a paragraph of updates about dd, and news of home, but i also make sure to talk about he and i and what's on my mind etc.
this is his first deployment since dd was born, so i don't know yet how we'll adjust when he comes home. when it was just the two of us, each time he came home we took things from scratch - we found out where our relationship was at, and what we needed, and went from there. trying to pick up where we'd left off weeks or months earlier was just unrealistic for us. people change, and for us it was more important to love each other through whatever changes than to maintain a certain way of life no matter what. good luck in figuring things out. i know it's tough.