The sub crossover should be either disabled or set as high as possible so that it doesn't get in the way of what the 990 is doing for bass management.

You mention that your choices are 0 to 180. That is the crossover and not the phase adjustment, right?

The 990 does have a way to lock the menus (most irritating when you forget that you set it, but potentially handy for adventurous system users). Doesn't really help with the sub's controls, though. Maybe electrify the switches on the sub?