Missing each other is not a bad thing. It shows that the relationship means something and that you care enough to notice that something is missing in your life.
You must also realise that this is a very different feeling to that if you weren't together or had broken up and you miss them. If you break up then that sad feeling would hurt a lot more - because you know that you can't recapture it. But that also fades with time.
This sort of loneliness has a different feel. You are still connected and you are still together. I'm sure you talk oh the phone, text or email regularly.
Remember that missing him won't really change your situation. Its just a useless emotion really! If you aren't happy with it then you have to DO something to change it.
Hey, 4 - 5 Months ago, I meet my love, he lives in Sweden and I in Denmark.We see each other twice a month, most of the time we see each other from thursdays to sundays. I always cry when he leaves, or when I leave him, it's like 7 - 8 hours train ride each time, and we switch on who visits who, like, I just visited him, so now on thursday he'll visit me.
Try to think of the next time you will see him, It makes me happy to know we'll be together soon.
Also get an MP3 player with songs on that mean something to you both, maybe make a compilation of good songs for each other. I did this and yesterday I went home from him to Denmark, and I didn't cry once on the train, I was sad. But didn't cry, the mp3 I bought, helped a lot! Listening to the music he liked, and my own.
Also, make use of the technology available to you. I have used facetime and webcams. I saw him over webcam before we went to bed. It's not the same as cuddling him but just seeing him is something which helped a lot. Hope that helps.