It’s best to make adjustments on a case by case basis. This is usually necessary anyway because we all use guitars with different pickup configurations so we should be aware of the tools available to make adjustments. If you’re happy with the balance of both effects but you notice a discrepancy in level between active and bypass, then I would try adjusting the Program’s Out Gain. The available 12 dB of gain should be way more than enough to balance out an irregularities, but in the case that it’s not, the In Gain may be too low to begin with and you can add more volume there.
If you’re ever going to bypass one of the effects during a performance, a good strategy begins with bypassing preset B while working with A by itself. Adjust In and Out gain so that alone there is no difference when active or bypassed. Then, repeat the process with Preset B. Then add both together and make changes to the program as a whole.
Keep in mind, the same can be done with the inserts.
