Avoid using self-deprecating humor... If you show you can't respect yourself, that means she won't be able to respect you either...
Don't crack jokes all the time... That'll show you're goofy...
Finally, mix your humor with some sarcasm and light banter... however, don't get obnoxious or anything... Just tease her. So in this case, where she says "You're funny", you can say something like "Yeah, I know" or "So I've been told".