If the molex is plugged in, it should be running. You can just place your ear next to the pump (that reservoir looking thing on the radiator) and you should hear a faint noise.
Yep, you got it. Put as much as you can in the reservoir, then turn the pump on for a little, then repeat until the loop is full. ALWAYS make sure there is liquid in the pump, so it doesn't burst into flames (Just kidding, it can break...
I would definitely get at least 4GB of RAM (1600mhz) and drop the video card. You can use the onboard video from the motherboard.
Also, if you don't mind using the stock heatsink, I would drop the CPU cooler. The stock can get loud,...