You have to pump water into the center hole and the 2 outside holes are to let water flow out. You cannot block them off. The Swiftech Apogee is an excellent block and the simpler installation is in your best interest for your first water loop.
As for a pump, I would suggest these:
My #1 choice and really the best choice: Swiftech MCW655
http://www.frozencpu.com/ex-pmp-27.html
My #2 choice, and it is the pump I run, the Eheim 1250 which you can buy at any pet store/garden center. It is a 110V A/C pump so you either need a relay kit or you must remember to plug it in before starting your PC, but they are pretty much THE most reliable pump made.
The Swiftech pump is 12V and can be plugged into your power supply so that makes it much easier to use, and it is still an excellent pump.