Question about closed loops

[BCOrchidGuy]

When you are using a closed loop does the intake usually sit at the surface and the outflow usually sit lower or is it the other way around. If it is the other way around how do you keep live stock etc from getting sucked in?
Is there a standard size for a gph rating or will your pump (powerhead in my case) limit the water intake. I'm thinking of using 1" bulkheads on a Mag3 on a 15 gallon tank, two intakes and two outputs.
Any suggestions would be appreciated.

Doug