The second hole in the bottom of a skimmer can be linked to your main drain or a secondary water intake. These are for low water level conditions to keep your pump from running dry if your pool gets low. If it had been used, there would be a ball/float contraption that would close off the skimmer and force the pump to pull water from the lower source. If it is not currently rigged up, then it is just plugged off so it doesn't leak or collect trash. If they look bad you could try to pull them and replace them, just be careful not to break your skimmer housing in the process. My plugs are actually glued in with PVC glue because I did not use them either.
Regarding one skimmer pulling harder than the other, my skimmers do that too. The one closer to the pump has more pull than the far one. That's just a function of your plumbing configuration. I have valves that I can use to adjust, but I just let them pull as hard as they want.
There is usually also a third knock-out hole in the back of the skimmer that can be used as an overflow.
Hope this helps
