"everything is good except missing you" It depends on what you're trying to say. If you want to say that your boyfriend's presence has been missing from the environment,, then you can say it like that. But if you want to say that YOU are missing HIM, then it would be better to say "Everything is good, except I've been missing you." If I was your boyfriend, I'd prefer the latter. :-)

Everything is good except for missing you.

Everything is good except that I miss you :)