It comes from the idea that somebody is like an itch - very hard to ignore. So it basically refers to someone that you can't stop thinking about, and is usually used in a romantic context. It can be used in a negative way too - if you keep annoying someone, you end up getting under their skin as well.

It means..." When you meet someone and you are drawn to them . you can't stop thinking about them even when you don't know them. something about them sparks something down deep. your imagination starts to run wild and you are physically and emotionally altered.They fascinate you"..