I am a new GM playing Pathfinder. I am curious about perception. How can I have the players roll for perception without making them really suspicious? For example, if a trap is in the middle of a room and they fail to perceive it, then they know something is up and probably would be super careful, even though they really didn't notice the trap. Thanks in advance!
If you like, you can assume that characters are taking 10 on perception all the time and use this as their check.
If they want to specifically check then you need to give them a reason to take a cautious interest in the trap. That is, there must be something in your description of the room that calls out, subtly or otherwise, "Look at me!"
For traps, if they don't deliberately search, have the unlucky character roll perception right before triggering the trap. If they succeed they can step back.
For detecting an intruder, roll for the intruder's stealth vs. the characters' passive perception. (You can just ask to see the character sheets, if you don't have their passive perception on hand.)