2 H90s will certainly give you a lot of options! You can even use one of the H90s as an insert in the other H90 to change the order of FX and looper.

The Hot Switch and MIDI PCs are two different concepts. Let me clarify:

When using Hot Switches you are not loading a new Program. You are simply changing many parameters of the current Program at once using a footswitch. Example: Use the ModEchoVerb algorithm. Start with a sound that has some reverb but no modulation. When you turn on Hot Switch 1, you can map the modulation parameter to this switch. So you can change the sound of your Program/Preset, without loading a new Program/Preset. Many of the factory programs have built in Hot Switch assignments, if you go to Perform Mode you can explore these.

https://cdn.eventideaudio.com/manuals/h90/1.7.1/content/edit-modes/parameters.html#hotswitch

MIDI PC messages will simply load a new Program. Example: send MIDI PC 20 to the H90, this will load Program 20 from your Playlist.

I suggest trying the Hot Switch option because this will allow you to alter the sound of Preset A while Preset B takes care of the looping. If you load a new Program using PC messages, this will stop whatever loop is happening on Preset B.