I'm currently running a server that mainly relays email to other email addresses. I have procmail setup for users that are have their mailboxes on the server, but how do I setup spamassassin to deal with these aliases emails? I haven't found a good set of documentation on the web addressing this issue, although I admit I may just be missing something.
You'll want to set SA up using a MTA layer integration, instead of calling it from procmail (which is an MDA and doesn't get called for relayed mail.)
What options you have available to you depends on what MTA you use, but most of the options are covered in the wiki:
http://wiki.apache.org/spamassassin/IntegratedInMta