I have the Anthem AVM60 and have found I don't need independent sub adjustment. You can run a "quick" one time measurement with Arc on any speaker, move it around, until you get the best pre results before running Arc. For my 3 subs, I turn them off and test each one alone, adjusting position, phase, and levels to be around 72dB each. Once each one is done, you turn them all on and Arc measures and adjusts the combined settings. Works wonderful and I can't ask for better results.
Now that Arc Genesis is out it is even better. You can go back after you've already uploaded your results to the AVM60 and just run an individual sweep of that speaker. This is handy if you experiment with moving your mains around or whatever.