One of the drawbacks of this hobby is that, for speakers to operate at their optimum, they need to operate in open space, without surfaces nearby to cause problems. So for best results do NOT place speakers, subwoofer included, in cabinets or entertainment centers.
Alan, Axiom's resident expert, had
this to say in a recent thread. He's talking about the M22s, but both are rear ported speakers, and the principle is the same.
For most of us, who live in the real world, circumstances (like WAF, size of room, furnishings, etc.) preclude doing what is best, and we have to bite the bullet and make do with what we can get away with.
To answer your question, the M3s would do fine with just the sub, but might be lacking in a room that size. And, with both the sub and the M3s in an EC, the results would probably be less than stellar. Only YOU could tell if you would be dissatisfied with this arrangement.
If you can fight the good fight without it destroying your marriage, as the others have recommended, I'd stick with the M990s.
