First make sure that you have designated your MMT as the motor mount. If you haven't, what I'm about to describe won't work.
1. Click on the Motors & Configurations tab
2. Verify, on this page, that your motor mount has a check mark by it (left part of the screen).
3. Click the New Configuration button (at top).
4. Now double click the "None" in the left hand column
5. On this new page, verify/select your parameters under the Motor Filters tab
6. At this point you can go over the right hand column and select a motor or type in what your looking for in the very bottom window.
7. Click "OK" once your done and OR takes you back to the Motors & Filters page.
8. At this point, I just select the Flight Simulations tab and takes me to that page
9. From this page I run my simulations with that motor.
Hope this helps!