Dave,
Since you like Maggies and you're in Austin, here's something to chew on.
The smaller Maggie (MMG) runs app. $600, direct from Magnepan with a 60 day return policy. Coupled with a good subwoofer (or 2) and controller, these little panels can be terrific. As it happens, the excellent Rythmik subwoofers are sold direct by Rythmik (also w/ a return policy), located in Austin. You could order a pair of Maggies and try them out w/the Rythmiks. If it doesn't work for you, returning the stuff (particularly the subs) is simplified.
As to controllers: I use the Velodyne SMS-1 controller @$450, (ocassionally set up with MMGs). I think it's a pretty amazing device, but many report that the $700 SMS/Audyssey controller is superior. Both allow digital room correction of the subs which IME will likely produce bass performance superior to any non-corrected speaker at any price. Depending on how low the MMGs go in your room, you might let them just roll off naturally and "snug-up" the sub below them - an approach many purists prefer.
OTOH, you may want to think about actively rolling off the bass from the MMGs. If so, budget another $300 (or more) for an active high cut unit, since the high cut in the Velodyne is both inflexible and digital. It converts the signal for DRC processing via an ADC and then back to analog. For me, this is fine for the sub's signal, not so fine for the main signal path. If you choose the SMS/Audyssey controller, it has no built in x-over and will require an outboard unit, anyway.
I actively roll my mains with the NHT x-2. The benefit is that you can choose any crossover point you want. Since the worst room issues are often around 80hz, you can cross a little higher and send these frequencies to the subs. That way you can use the DRC in the sub controller to address those issues. BTW, I've found via direct A-B comparison that the X-2 (the only intrusion between your amp and the MMGs) is completely inaudible to me. However, I'd be the first to acknowledge that this doesn't mean it will be inaudible to everyone. As always, YMMV.
Total budget for a pair of 12" subs, NHT x-2, Velodyne SMS-1 and Maggie MMGs is app. $3K, add another $250 for the SMS/Audyssey. As I noted, I have used this exact set-up. Since the sub controller can remove the most audible room to room variations (those below 150hz), I can pretty much assure you terrific results.
Good Luck
Marty