I get the whole stealth vs perception DC (perception DC is 10 their perception btw) initiative or otherwise rolls as the GM with a secret roll or as an PC against my creature's perception DC, but my question lies in if they are able to re-stealth behind cover against my perception DC again?

I have a rogue that gets out of cover shoots then wants to go back into cover and re-stealth is the reason I'm asking. My problem with this is how do I go about targeting this rogue with spells or attacks, or can I. I realize the cover rules are 1 AC for light (behind a person) 2 for moderate 4 greater. The other thing I'm wondering is does he gain the hidden dc 11 flat check that I've read about?

Stealth has me all confused, and I want him to be able to do what makes him useful, but I want to get it right.