ILS frequencies are tuned on the pedestal, and I have never had a problem with that.  (I think they are actually using one of the VORs because of the way flight sim is set up.)  I often manually tune my nav radios and have never run into a problem, of course you have to change them to man from auto.

As for comm frequencies, I make my co-pilot in Radar Contact handle comms, so I guess I've never run into it one way or another.

The APU problem is a problem, but there's a thread on that already, I think.