most perception rolls you roll when presented with "stimulus" this includes someone sneaking past you, because they might be making noise, etc. If you fail, you don't get to make another perception check until the conditions change (a gm call) or until you spend a move action to actively perceive your area. So the first is a freebee, the second costs you (if you're even aware enough to use it. Using the move action most often happens in combat when you see other people reacting because they made their checks).
In answer to your question, You realize where his is when he tries to sneak past you, because that is the most dangerous point where he can get caught, i.e. the rogue determines the risk point. If he didn't sneak past you and stayed behind cover, you still roll perception because he might be making noise or some such. In that case you might know "someone is there", but can't pinpoint them. In any case, the GM calls for the number of rolls.
I agree with you about avoiding too many rolls. I might have one stealth roll for operating behind cover/concealment and then just roll whenever someone tries to hop between cover/conceal or tried to sneak up and stab someone.