You are right, not all settings are saved per 'preset'. The values behind the rotary knobs will always be set to the real rotary positions when you change to a different 'preset', regardless of the settings in the editor. The values in the editor are just there to see the current settings without having to look at the amp, to remote control the amp from the control room or something like that.

This might look a bit limiting at first but this strict two channel separation is the whole concept of the amp when used in stand alone mode.  There are no complicated choices to make and you'll always see what you get - just like with every other amp. And other amps with massive switching options have the same problems with unpleasant eq settings and volume matching (thinking of Mesa Mark V, Roadking etc). But once you've set your dials you're done.