I have two skimmers. When I opened up the pool I pulled the plugs out. In front of where the plugs screw in that I removed (the tall plugs that kind of look like a liter bottle) there is another plug. On both skimmers this plug is still in place.

Should it be?

do you have a main drain that's connected to the skimmer(s)?

Not quite sure what you mean but I have 3 valves leading into the pump. L and R skimmer and main drain.

There are two ports or holes in both skimmer boxes. The ones furthest from the pool are open and the ones closest are plugged with a flat square slot plug.

The problem I have is I run a Kreepy Krauly (came with the pool) and I assume I would have to plug the hole in the skimmer every time I run the KK. Not that this is a big deal.

You answered my question. You do have a MD but it has it's own piping back to the pad. Don't remove the plugs. They stop up the holes that don't go anywhere.

Great. Thanks Bama!