There's a few different ways you could go about this, we had to do something somewhat similar.
In my situation we're a site within a bigger commercial site, which has it's own user auth/reg. When a user logs in or registers on our page, they're sent thru the global auth/reg process, and then redirected back to our page. What we do in the background is create a WP account for them & set a WP cookie, so that they then have access to whatever WP functionality we allow. They never directly have to login to WP per se, it's done for them so long as they're logged into the "main" system.
Essentially this just means that in short:
if they're cookied with main site: find matching user acct in WP , cookie them, else create acct for them in WP.
Depending on how many user records you have, and what else you're doing with your existing user db, you could simply write a script that loops thru your current db & inserts a user record in wp_users. If you're only storing username, pw & email, I'd say those "not so important" fields & anything "extra" you want to store for your users could simply be stored in wp_usermeta. (wp_usermeta is invaluable in my experience :)
That's just one approach. As Richard mentioned, you could also just fiddle with hooking into the existing user auth functions, if you don't want to create user records in wp_users. You'll probably at least need to set the wp cookie & all that, I would imagine. But I'd say if you don't have tons of data, just move them into wp_users. You can still user your existing login, and do the WPMU stuff in the background.
Hope that helps!