I think the easiest way to do this would be to have three separate departments, one for accounts at each webhost. You may be able to tweak the WHMCS templates so that a "server" dropdown in the submit ticket page will submit the ticket to the appropriate department/end-user support API, however I'm not sure how easy this would be to accomplish.
This could be done depending how the End user Support is handled. I guess you could edit the 'submit ticket' templates to either force the tickets to the correct department based on the server they are installed on or allow them to choose a department name that is coordinated to the server/service.
I think the first option would be less confusing to a client.
**edit** Yeah, what he said above! Didn't see your response when I clicked submit!
Innohosting uses a custom integrated system to handle end user support. Their system edits the WHMCS template files in such a way that you don't handle tickets through WHMCS, you have to use their end support desk. Therefore it seems to me that you would not be able to use one WHMCS installation to handle support for all 3 companies.
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The main thing I want to avoid in this endeavor is the need to make three different brands essentially managing three different companies. I'd like to accomplish this if possible to keep everything under one domain/company.
Maybe the best idea would be to check with a WHMCS add on developer/programmer? and get into a convo with Othio/Inno/EZPZ, myself and said developer?