You are correct that the crossover is preset with no adjustment.
Since the amp/controller only has RCA line level connections and the 500C has no preamp out, but does have a tape out, are you connecting this tape out to the amp/controller? If so, that would explain the independent volume controls. It may be a possibility to use a speaker level to line level adapter on the speaker outputs in parallel with the speakers to drive the amp/controller. I have done this with solid state amplifiers, but not tubes. Im thinking it should be OK, since the impedance load of the adapter is very high. This would allow you to use only the 500C volume control. The amp/controller VC would then be used to match levels between sub and speakers.
Since the amp/controller only has RCA line level connections and the 500C has no preamp out, but does have a tape out, are you connecting this tape out to the amp/controller? If so, that would explain the independent volume controls. It may be a possibility to use a speaker level to line level adapter on the speaker outputs in parallel with the speakers to drive the amp/controller. I have done this with solid state amplifiers, but not tubes. Im thinking it should be OK, since the impedance load of the adapter is very high. This would allow you to use only the 500C volume control. The amp/controller VC would then be used to match levels between sub and speakers.