Hello,
To give a basic understanding of the H9000 architecture: There are 4 FX Chains, and each FX chan can run 4 algorithms. The algorithms can be routed in series/parallel in many variations.
The FX chains may use an combination of the inputs/outputs. The image below shows a single FX Chain with 4 algorithms in parallel using 8 channels of USB audio. Each of these algorithms can be thought of as a stereo processor, there will be no crossover between the channels. You could send your guitar to Blackhole, and your drums to the Micropitch, for example.
This is only using 1 FX Chain, you still have 3 more chains and USB channels 9-16, and even more I/O using analog/digital/expansion cards.
If you were to compare it to using the Eclipse in dual mode, it would be like having 8 Eclipse units in 1 box, with a great remote app that makes everything quick and intuitive.
Let me know if that clears things up, there are countless ways you can use the H9000 depending on what you are trying to achieve with your setup.
