How do I tell whether rules in my user_prefs file are active?
When SA is working well, the user_prefs file is referenced for parameters (such as Bayes on/off), score adjustments, blacklists, whitelists, and the like.
However, according to http://www.spamassassin.org/doc/Mail_SpamAssassin_Conf.html#privileged%20settings rules are not executed from user_prefs files unless a) the allow_user_rules setting allows this (rare), or b) you execute SA directly rather than through spamd/spamc.
To verify whether rules within user_prefs are executed, in that file create a rule like:
(Use your own email address instead of Gordon's.)
If the rules in your user_prefs file are active, this rule's name should fairly quickly be displayed in the SA headers of emails addressed to you.