Hello,
The H90 will automatically process your signal in mono or stereo, or mono in > stereo out / stereo in > mono out. This is all configured depending on which physical inputs/outputs are connected to the H90.
The most noticeable difference will be whether you are using the stereo output of the H90 or not (the effects will produce a nice stereo image when you are using stereo outputs). Some effects (certain delays, Harmonizers, etc) have individual delay lines for the L/R channels. So if you are using the pedal with a stereo input/output, and you only send a signal to the left input, you will only be using the left channels effects processing.
I would suggest giving your setup a shot and trying a few programs/presets that use various algorithms and see how you like it.
Let me know if that answers your question.
