The only way to gain confidence in this area is by practicing, and really, flirting is only about being especially nice to someone, and being comfortable when you do it.
I suggest you start by flirting with girls you like, but don't really care about. For example, if you graded girls on a scale from 1-10 (which I ordinarily hate, but am using it for illustrative purposes), try flirting with the ones who you'd rank 4-6. This way, you can aquire some skill. When your confidence improves, then you can move on to girls that you are more interested in.
You won't be perfect initially - no one is - but you will get better with practice.
Relax... I'll need some information first. Just the basic facts - can you show me where it hurts?