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!!
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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
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. 
Pure Stereo is "Pure Stereo", use the "2 Channel" selection. I’m pretty sure that will include the subs.. I don’t use Sub out, on anything.. I just split the signal on the mains.. It’s the best way to get a full signal for the subs, too. You won’t have "Sub control" on the AV unit BUT you will still have loudness, bass tone control, and of course volume. Any other settings, like XO, (60-80hz or below) phase, gain, and any OB PEQ or full blown DSP. Use the subs.

When you enable the onboard Mac Bass system, that CAN cut the signal to your mains.. make sure they are set to "Large" speakers too..

That is an option or two..

BTW, I’m a Mac guy, no smack talkin’ from me, I own um. I love um... 50 years this summer.. Wonderful product.. Great support. (2) MX110, MX120 and MX121. The 120 is one of the BEST three speaker set ups around.. and or course the MX110z.. just one of the best preamps/phono stages EVER made for the money.

Tough to beat a Mcintosh. C, MC and of course the MX series.. Mac 1700 and 1900. not so much...

Regards