I've been getting more spam recently so I did sa-update for the first time in a 
year (I thought it was automatic :-()).

I restarted the spamassassin service (Ubuntu).

$ /var/lib/spamassassin$ ll
total 16
drwxr-xr-x  4 root root 4096 Oct 15  2011 ./
drwxr-xr-x 45 root root 4096 Jun 12 06:40 ../
drwxr-xr-x  3 root root 4096 Aug 27  2011 3.003001/
drwxr-xr-x  3 root root 4096 Sep 21 23:59 3.003002/

Will it use the latest rules or do I need to delete the older ones?

Where in a mail header does it say what version of the rules it used?
X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on mail
X-Spam-Level: ***
X-Spam-Status: No, score=3.2 required=5.0 tests=BAYES_40,HTML_MESSAGE,
        RCVD_IN_BRBL_LASTEXT,SPF_HELO_PASS,URIBL_BLACK autolearn=no 
version=3.3.2

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