the 6cu is good. it will cool that thing fine, especially if you are not overclocking.
if you use even the white stuff that comes with the heatsink, it will be fine...but if you want it a few degrees cooler, i would say use arctic silver...
as for the case, what i would do is test it. then try it with the holes that you mentioned sealed up. cover them with tape or something.
sometimes having holes in the panels like that can kill the controlled air flow in the case, causing the fans to be innefficient.
test it both ways, because maybe it is designed to have those.
-DAvid
-Live, Learn, then build your own computer!-