Well, I think having too many options is a good problem to have! I would say the most accessible way, and the way I'd do it, would be to use one knob rather than two to select the bank. It'd be easier to keep track of that way.
Using your UI, you could let the user decide if each of the banks had 4, 6, or 8 patches (depending on patch size). This way, when holding down the Push button, each of the four knobs would allow the user to scroll through a bank and flash according to the divisions. Considering Owl users are limited to 4 user patches currently, I think very few people would need more than 32 unique patches at a time. I think it'd be much easier (for me, at least) to remember that the patch I want is knob 3, all the way to the right, or knob 4 all the way to the left, instead of counting flashes between two knobs.
I'm sure there are simpler ideas, but that's what I came up with.