You won't see too much of a difference - the hyper 212 comes with decent paste.
(The stuff you want to avoid is the white sticky "paste" that looks like glue.)
I couldn't answer your second question without you telling us more about your scenario, but I can say that having two fans on the heatsink, unless they're exactly the same, can cause problems. I'd have an input in the front, and outputs on the top and side.