To set the RF id, go into "configure home" click on the mrf-260 in the left pain and click properties at the bottom.

You can turn IR and RF off an on per device. So if you want IR on your TV and RF for your integra you can these individually under "Program" and then "RF Control" using the "Signal" dropdown.

I would definitely test using an emitter first if you are having problems because the emitter will light up when you send a signal to let you know you are routing to the right ports.

I would think using fixed ports would be fine for this but I haven't used an MRF-260 in a long time. I vastly prefer the 350's