Down-firing Sub makes floor rattle

Yeah, you're really not going to be able to solve this, other than balancing the sub out properly in the first place. Basiclally, down-firing, front-firing, slab, no slab, or even suspending the sub in mid air for that matter, isn't going to do anything about the airpressure and bassmodes in your room from being excited!!! Basically, unless you do something to your floor, it's going to respond accordingly. That's how bass works.
conversly, people think if they move their sub out from the walls, that it won't be as boomy in the room next to it. WRONG!!! That's not how it works.
Acoustics are what they are. You'd need to, like I say, just make sure you're sub is balanced out in level with your mains/the rest of the system (other than sub being way louder than the mains), and add some mass to your floor!
Good luck

1 more thing....the manual says the crossover on sub should be set at 70% of main speakers lowest frequency...so if my speakers go down to 56 hz, the crossover on sub should be set to 39hz...does this make sense? that leaves a huge gap between where mains leave off and sub picks up...i am assuming martin logan knows what they are doing but this doesn't make sense to me....... what do you guys think?

Yes, it makes sense. You sub rolls off gradually above 39hz, your main speakers roll off gradually below 56hz, and the combined energy from both speakers between 39 and 56 hz will equal the out put on either speaker alone at the roll off frequency. BTW, this assumes that the crossover network you are talking about is the one built into the sub. An outboard crossover network not specifically made for your sub might have different slopes and require different frequencies.

Shadorne's point about other sources of rattle and ways to cure it is right on. I had a framed picture on the wall rattle and I wasn't even being overwhelmed by the bass. Thought it was in the electronics/speaker. Put some soft materiel between its bottom edge and the wall to fix it.

Flrnlamb is also correct about the sub's drivers position not being particularily relevant.

update........lowered the crossover to 39hz, huge difference, sounds much better...also, kept it downfiring, but put the spikes on, also definite improvement...now just trying to fine tune the volume...gonna listen like this for awhile, then try to front fire...see what happens.....i really do like this sub and may just get another for stereo subs...what do you think?

An Aurelex foam platform should do the trick. This was very effective in taming the 160 yr. old sprung floors under my Vel DD-15.

http://www.auralex.com/sound_isolation_gramma/sound_isolation_gramma.asp