the problem is i don't know where to start, in my current squirrel on debian, email users are system users, i was hoping this setup will work with roundcube in my freebsd box, but it doesn't, i've looked at the logs, but i can't see anything pertaining to dovecot or roundcube for that matter.
I've got it running on OS X server (it's like freebsd but we spend a lot of time trying to lock the GUI out from touching our files:) ), both tested right on the localhost and a separate server -- regardless, I still think you're confused on exactly what this can and can't do.
This thing really is just like an application itself, pretty much what everyone is getting too. You can install it on whatever web host you have the mind too so long as you:
You add the mysql tables into your database via the mysql.initial file supplied by the developer.
Then you add the database values in the db config file, and put in your mail values in the main config file. That's it -- the main config file takes values like you would any application -- in/out server, server authentication method, domain, etc. You can set it up to read multiple domains if you'd like, but it's not going to matter so much unless your mail server reads those domains as mail domains.
So it DOES use system users, just like any other mail application in the world uses system users on a server, so long as you've given them mail ability. But it does NOT do any advanced functions like change your password, etc. It's just a remote application that everyone uses, the values you supply are simple mail values -- unless I'm confused by your statement, I think you're just over thinking it:) It's not married to the system in any way except the values you tell your server it's allowed to submit to that application for mail enabled users.