Yes it would be nice to have a way to octave-shift one or both layers when using stack or split; for now, must save a separate version of the program(s) with oscillator pitch and filter cutoff changed. In that case, I'm storing the layer B program in the next program slot after the layer A program, so that I don't overwrite the original program that layer B came from. Changing the name of the stored program helps remind that it's a "layer B" program.
btw as a way to keep the two layers together on the computer, I've tried storing this sequence in one file:
MIDI control change 80 value 0 (choose layer A)
edit buffer SysEx dump for layer A program (with stack or split mode chosen)
MIDI control change 80 value 1 (choose layer B)
edit buffer SysEx dump for layer B program
Seems to work, since internally OS version 2 must have separate edit buffers for each layer (after the stack or split program is initially recalled, you can temporarily change parameters of one or both layers without affecting the stored programs, unless those are saved again). An incoming edit buffer dump populates the active layer, and an edit buffer dump request will return the program dump from the active layer.