Now you have me confused. Let's clear some stuff up:

You have an MX-980 in the theater with an MRF-XXX kit, right?

You then carry the MX-980 remote upstairs to the bedroom to control through the "cheap-o" IR extender for the local bedroom cable box?

If the assumptions above are correct. Create 2 devices of the cable box. One for upstairs with IR only enabled in programming and one for downstairs with RF only enabled.

If not, you need to be more specific as to exactly what devices, sources and the like are in both areas.