Beginner's question...

Once mail has been “examined,” it is either in your Inbox or in the Spam folder. How do I then run other rules on the mail in the Inbox?

Thanks.

Which mail program are you using? In general, the procedure is to put the SpamSieve rule at the top of the list. The spam messages will be moved to the Spam mailbox, and the other messages will be processed with the remaining rules. With Entourage, you need to setup two SpamSieve rules in order to filter the non-spam messages with your other rules.