You could get away with the single 1.5" drain, but if you do the dual 1" drains you could use the Herbie method for basically silent draining:
http://www.reefcentral.com/forums/showthread.php?s=&threadid=344892&perpage=25&pagenumber=1
Also, I would probably want more than two holes for closed loop. If you are going to use a Dart, I would do a single 1.5" intake hole to the pump, and put it someplace where you can put a strainer over it so it doesn't suck up fish, and make sure its someplace where you can get at it to clean the strainer once in a while. Are you going to use Ace's style of "floating reef", with a bunch of PVC spraybars to return the CL, or are you going to just use loc-line or something? In any case, I would lean toward three or four 1" returns from the closed loop with that much flow to spread it out more. 3600gph coming out of a single bulkhead is going to be hard to diffuse.