The first year was by far the hardest for us. Year two is harder for a lot of folks, but year one was the doozie for us. Things do get better with time and consistent work.
I think discussing these feelings as they come up may be difficult at first, but having them out in the open could be helpful.
Is there a way you can stay in touch that makes him feel more comfortable about being away? Skype sessions with you and the kids? A random text telling him how much you love him?
Hang in there and keep working at it. It can and will get better.