1) From what I have seen, SqWebMail seems tied to using Unix system users. Is this the case?
No.
2) Because these users aren't proper system users, they don't have a home directory. Because of this, the Maildirs are stored on another server to the one running SqWebMail, and are organised by the path: <domain>/<1>/<2>/<3>/<username>/Maildir where 1,2,3 are the first 3 letters of the username. Is it possible to set up SqWebMail for a system like this, which is on a separate server?
No.
