Welcome to TFP!!
The second line can be used for 3 things (anyone who uses the first 2 is a moron

)
#1 A balance line (as per drjames) as was said it's a below water line that "supposedly" keeps the water in the skimmer at the same level as the pool. It's a great idea on paper but the pump is drawing more water than the atmospheric pressure can refill - hence, the skimmer doesn't refill, air is sucked into the line and the damage that this is 'supposed' to prevent happens anyway. (they are also a PITA to winterize!)
#2 Plumb a main drain via the skimmer (as per Jason) - :grrrr: :grrrr: :!: What a moronic idea!!! The valve in the skimmer to control the flow between the skimmer and main drain is highly susceptible to failure and if the main line from the skimmer breaks - you are SOL! Also, it's far better to have the suction lines separate - it allows more flow to feed the pump. It also has the same problem with keeping the skimmer 'fed' with water if the water level drops. It's also a PITA to winterize!
#3 A reserve line - this is about the only option that makes any sense. When you plumb the pool you run 2 parallel lines from the skimmer to the filter pad, you only plumb one to the pump, but leave the other stubbed up (capped and plugged) to be used if the original line fails for whatever reason. The problem with this is that since the pipes are run together, what breaks 1 will probably break the other, unless it's freeze damage and the reserve line has been kept dry.
As far as I know those are the only reason for the second port in the bottom of a skimmer, if yours is open it's not a reserve line.
For winterizing it needs to have the water blown out of it and be plugged. If it is a balance line or a main drain line, let me know and I'll tell you a way to winterize it
