HoSStiA - The default thread mask should work fine. vbSEO renames your URLs, but leaves vBulletin's thread structure intact. A quick example using vbseo.com:
*vbSEO thread URL:
http://www.vbseo.com/f55/subdomain-41325/
*standard vBulletin thread URL:
http://www.vbseo.com/forum/showthread.php?t=41325
Both URLs render the same thread. So, the mask would simply be
http://www.vbseo.com/forum/showthread.php?t=%thread_id%
I'm happy to check out your site and let you know how to setup the mask. PM me an URL for a random thread.