Hm... In general, I don't think they have many sleeping habits to get used to (though I fully believe Alistair snores like the middle-aged dad he is) but perhaps 3 had to get used to Alistair having the bedroom bloody cold, like freezing cold (that man almost never turns on his heating. it costs a bloody fortune), and Alistair had to get used to 3's restlessness in bed (timelords need less sleep than humans tbf, and his mind goes a million miles an hour).
Due to the fact that 3 is a Timelord (who eventually gets his TARDIS fixed, but also just.. travels around the world when he gets the itch) and Alistair's job requires him to occasionally travel to other countries for whatever reason, I think they're both used to being away for long periods and it doesn't often bother them as such. They go about their lives, Alistair looks after his daughter or goes to the pub with Yates and Benton, and 3 spends time with Jo on fantastical planets or stops by to see Liz or such
When away doing bother them, they both tend to dive head-first into work as their way of dealing with anything bothering them, but it helps pass the time until they next see each other, and because they work together and the nature of their jobs, I feel like it oddly makes them feel closer to each other.
I think eventually 3 might create a way that they can ring each other, even if 3 is on another planet at another time. That also helps tremendously. (they'll never admit it, but they miss not being able to bicker, and Alistair misses not hearing 3's bizarre alien experiences and celebrity encounters, and 3 misses hearing about how Kate is doing and how the garden is coming along)
