M,
If this is an older pool, then one hole is from the main drain and would not have any suction. The other hole is from the pump and should have a ton of suction.
Generally the little flap turns on the main drain if the water coming into the skimmer drops below the skimmer entrance.
Main drains, when plumbed into the bottom of the skimmer are more of a pain than any real value. Since a main drain is not needed, most people just don't use them.
If your main drain is plumbed back to your equipment pad with its own valve, then the port with no suction is usually plumbed right into the side of the pool, just below the skimmer. This pipe is used should the water level fall below the skimmer mouth.
Thanks for posting,
Jim R.