Many manufacturers (even high end like Wilson) use that exact design (monitor on top of woofer). No problems.
Yes dual opposing/sealed woofers is ideal but not required.
Yes monitor placement is almost never the "right" placement for woofers, but virtually all the "big boy, full range designs from high end vendors" do it.
In any room, the most to least ideal is to have:
- 4 subs spread around the room (search swarm/ DEBRA)
- 3 subs spread around the room (if you just can't run that 4th cable or afford the 4th sub)
- 2 subs, the 2nd being a black hole absorber (sub with microphone to sense and counteract standing waves at opposite end of the room):
http://www.spatialcomputer.com/page9/page10/page10.html- 2 subs at opposite ends (long wise) in the room, rear one wired out of phase
- 2 subs located under monitors, in phase of course
- one sub "properly" located in the room
- full range speakers
- less than full range speakers