Personally I would put these lines in your local.cf file (to make the changes server wide rather than user specific):
This file can usually be found in /etc/mail/spamassassin
Note: You will need to log into your server using somthing like WinSCP (if you are a windows user), or edit it in VI if you are a masochist 
use_bayes 1
bayes_auto_learn 1
bayes_auto_learn_threshold_nonspam 1.0
bayes_auto_learn_threshold_spam 10.0
bayes_file_mode 0777
# Limit the size of the Bayes database to about 30MB (in my case)
bayes_expiry_max_db_size 500000
# New Bayes Rules for even more certainty
body BAYES_99           eval:check_bayes('0.990', '0.999') 
body BAYES_999          eval:check_bayes('0.999', '1.000') 
body BAYES_00           eval:check_bayes('0.001', '0.010') 
body BAYES_000          eval:check_bayes('0.000', '0.001') 
describe BAYES_99       Bayesian spam probability is 99 to 99.9% 
describe BAYES_999      Bayesian spam probability is 99.9 to 100% 
describe BAYES_00       Bayesian spam probability is 0.1 to 1% 
describe BAYES_000      Bayesian spam probability is 0 to 0.1%
# My Suggested Bayes Scoring
score BAYES_999	3.000 
score BAYES_99	2.500
score BAYES_95	2.000
score BAYES_80	1.500
score BAYES_60	0.500
score BAYES_50	0.001
score BAYES_40	-0.100
score BAYES_20	-0.200
score BAYES_05	-0.500
score BAYES_00	-1.200
score BAYES_000	-1.500
# Ignore headers which may cause trouble
# PICK WHICH ONES YOU TRUST!
bayes_ignore_header X-Bogosity
bayes_ignore_header X-Spam-Flag
bayes_ignore_header X-Spam-Status
bayes_ignore_header X-Spam-Virus
bayes_ignore_header X-Spam-SpamTokens
bayes_ignore_header X-Spam-HamTokens
bayes_ignore_header X-Received-From-IP
bayes_ignore_header X-Virus-Scanned
bayes_ignore_header X-Spam-Level
bayes_ignore_header X-Sender
bayes_ignore_header X-Mailer
bayes_ignore_header ReSent-Date
bayes_ignore_header ReSent-From
bayes_ignore_header ReSent-Message-ID
bayes_ignore_header ReSent-Subject
bayes_ignore_header ReSent-To
bayes_ignore_header ReSent-Date
You can learn a LOT by reading the spamassassin mailing list which is available online at:
http://www.nabble.com/SpamAssassin-f191.html
And by reading the wiki at:
http://wiki.apache.org/spamassassin
Hope this helps 
