McIntosh MX160 2 channel with Roomperfect


I own an MX160 and relocated from Tx to Mi. My system was all set up there; however, with the move I have an issue that needs to be resolved.  The room perfect works great; however, during set up I entered my 2 Martin Logan Force subs.  I have 2 a left and right.  It sounds wonderful for every sound setting except 2 channel where it cuts out the subs.  So I am missing the deep base when I want to listen to channel.  The rest of the music sounds great it is just the deeper base I am missing.  I want to run the 2 channel with the subs.  Makes for a much smoother all around sound.  So if anyone has any tips on how to get the MX160 to run the subs on 2 channel I’m all ears.  My goal is not to have to set up another room perfect for 2 channel. 
Appreciate any suggestions/tips!!
woots
Thanks. As you say 2 channel is 2 channel.  My issue is that because it is only playing 2 channel and no subs I’m missing out on a significant of bass. This is because the Roomperfect directed most of the bass below a certain frequency to the subs but since they aren’t playing with the 2 channel I’m missing that portion of the signal.  
I will do like you said and make sure my speakers are set to large in the setup. 
I, like you, am a Mac guy and I really appreciate your feedback. 
No OP, my Macs have a "Pure stereo" and a "2 channel" setting.
The "2 Channel" setting will let the subs (if they are hooked to the sub output) work also.. In "Pure Stereo" my subs do not work.. 

I don't use the sub out, I split the mains L/R and use that for the sub input.. Not the Mac Bass system.. 

BUT, room correction does make it easy. I just don't use it..

3 speakers is about all I can stand I like analog, not into digital correction... 3.2-6 is pretty close. Just depends on what I'm doing..
2.2-4(2) Two mains, 2MB columns, 2-4 subs.. I'm not a surround guy..

Regards