Using your own radio is very possible, I have successfully done this with my DX6.
Your dual rate toggles will work just fine but that isn't your starting point. Once you turn off or modify the other settings your dual rates will work.
1: I suggest reading the inertiasoft faq's for your radio set up.
2: Read back several pages for a discussion about changing channel assignments.
3: The idle up switch on the wrong side is nothing more than a channel assignment and is the same problem with the hold switch.

If you do change your radio to emulate the trac contoller, make sure your radio is in heli mode, (having your radio in aircraft mode is for emulating the FSOne's radio controllers only) and that you turn off any CCPM in FSOne. Read back a few posts to see more info about this, I'm pretty sure I posted info about this.
Post again if you have questions and I'll try to more thorough.
Good luck
Scott H.