Geno, the only dumb question (IMHO) is only the one you don't ask.
You will need two pumps. One is on the skimmer itself, whether you're using it as a HOB model or "in sump" model. You'll need a pump with that. Depending on the skimmer you go with, some come with pumps and some you buy the pump separately (or upgrade to a better pump).
Then you will need a bigger pump for the sump itself. That's to push the water from your sump/refugium back up into the DT (Display Tank). Usually you put this bigger pump into the "return" section of your sump/refugium.
As for the two drilled holes in your RR tank, one is generally for the drain line (water going into the sump/refugium from your DT) and the other is for your return line (water coming from the "return section" of your sump/refugium back into your DT).
You'll need bulkhead fittings (if they aren't already installed) in there so you can hook up the drain & return lines to your DT.
Do a search on the forum for sump and/or refugium and you'll come up with a lot of information. Some people even post up photos of how their setup is done and descriptions of what went where. That's what I did while I'm setting up my 90. I would post up my photos to help you, but it's not exactly completely done yet, so that won't help ya. LOL
