From factory, the H90 runs in Insert mode, where I/O 3&4 are used for inserting external effects in the signal chain of the two Eventide algorithms. If you want to use the H90 like two independent mono or stereo effects processors, like you describe in your original post, then switch the H90 to Dual routing mode. I/O 1&2 will have its own path and 3&4 another. On a program basis you can store effects on either path depending if you’re at a gig (I/O 1&2) or at home (I/O 3&4). It would be possible to run I/O 1&2 at instrument level and I/O 3&4 at line level when connecting to your audio interface.
You would benefit from going deep into this topic by watching this video: https://youtu.be/0G_WtfUatSc?si=4YN7iveUwEtnjk5C
