will the H90 know how the handle the mono -> stereo aspect of the presets based on which path they are on?
Yes. The key thing to remember in Dual Routing mode is that anytime I/O 1 and I/O 3 are used by themselves, things will function in mono. When outputs 1&2 and/or 3&4 are connected, the H90 knows to output signal in stereo.
I assume I would use Input1/Output1 for pre and Input3/Output3/4 for post?
In Dual mode, that’s what Eventide recommends but it’s really up to you.