We have trouble with this as well, though kind of in an opposite way :) Dsd is with us 4 nights one week and 1 the other week, and we have struggled with bedtime routines pretty much since dd was born! They are so excited to have dsd here that it kind of disrupts everything and takes forever to settle them down, plus dsd goes to bed later (she is almost 6 years older than dd, almost 9 older than ds) and it is hard to keep her quiet while i put the little ones to bed.
What we have finally settled on that seems to work really well is just to keep bedtime VERY consistent no matter who is there. We read the same amount of stories in the same place whether dsd is with us or not (we used to sometimes read in my bed, sometimes on the couch, get an extra story when dsd was here, etc.) We read in dd and ds's room (they share, dsd has her own), they say good night, then dsd goes into her room to read, work on homework, hang out quietly while I get them to sleep. It is harder to settle them down (as I imagine it is hard to do for your son when he is missing his brother :() but keeping things very consistent has made the situation much easier to deal with.
If your sons share a room when they are home, can your older relax quietly in another room while you get your younger son to sleep (your room, the living room?) As for dealing with the upset..it is hard :( We started singing a good night song where we say good night to everyone in the family, whether they are present or not. maybe this would help your son so he can still say goodnight to his brother when he is not there?
Good luck, it is hard to watch siblings missing each other on a weekly basis!