To answer your questions:
Emote is just the control software for the H9k; it does not automatically route audio connections when an instance of the plug-in is placed on an audio track. When using Emote as a plug-in in your DAW, only one instance is needed and all of your audio routing from the DAW to the H9k will need to be done the same way you would when using any external hardware processor. In Logic, this will be using the “I/O Utility.”
Yes, you can use the H9k as 4 separate stereo processors as you described. This doesn’t necessarily need to be done using the USB audio; the H9k has 8 analog I/O and up to 8 digital I/O using ADAT or AES/EBU. If you use the H9k as part of an aggregate device with your audio interface, the USB I/O will now show up alongside your audio interface’s I/O in your DAW.
You can clock the H9k externally via word clock as part of an aggregate device without any issues. When using USB audio, the H9k will show up as an audio interface labeled “H9000 USB Audio” in your Mac Audio/MIDI setup page. The H9k USB audio has a separate clock from the H9k’s internal clock, and the H9k USB audio has to be set manually in your Audio/MIDI setup page; it cannot follow an external clock source such as word clock. So, if you change your sample rate on your audio interface or DAW, the H9k and all of your other synced equipment will follow the clock of the interface, but the H9k USB audio will need to be changed manually or there will be a sample rate mismatch. When there is a sample rate mismatch using the USB audio, you will get an error message that says "USB audio muted" and you will need to correctly match the sample rates to unmute the USB audio.
When using the H9k in an aggregate device setup, you will need to make sure the sample rate of your H9k, the audio interface/daw, aggregate device, and H9k USB audio are all at the same sample rate. This may sound complicated but it is pretty easy once you get used to it. Having your H9k clocked from the audio interface makes it a bit simpler too.
The H9k does not currently have global clock settings, you will have to determine the clock source for each session. However, when you load a new session you are given the option to keep your current clock source settings, so you won’t need to be setting the clock source every time if you choose keep your clock settings.
When you load a DAW project and connect to Emote, you will be prompted to load the H9k session data for that particular DAW project. We also recommend to save all of your data as a session on the H9k itself in the event that the DAW project gets corrupted or there is an issue with loading the data.
Let me know if that clears everything up for you and I’d be happy to answer any other questions that might help you take the plunge!