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.
Yes this is an older pool. Thanks for your reply. Still not sure if I should cover the hole that has no suction or cover the one that has suction. or not cover either. I just want to make sure when my pump is running the water is filtering properly. thx
The flap will make absolutely no difference in your water being filtered properly.. Unless you cover the hole with suction.. if you do that, you won't have any water going back to the pump and your "filtering" will be zero..