If you have enabled the spam box option under SpamAssassin in cPanel, by default anything that SpamAssassin scores at 5 or higher will be diverted to a spam folder, away from your inbox. You can, of course, change the score threshold to lower than 5, or higher, but 5 is generally recommended. Changing this score will change the threshold for an email to be considered spam, for all email.
If you are still receiving a lot of spam messages to your inbox with the spam box enabled, you may have to tweak the scores assigned for individual tests to improve the filtering. SpamAssassin performs a number of tests against each message, with each test contributing toward the overall score.
If you view the headers of a spam message you've received, you should see a list of the tests that contributed to the score of that message, and what score was assigned for each test. If you examine the headers of several messages and find that one or more tests are showing up frequently, and the test itself seems like a test that will identify spam without causing false positives, consider increasing the score for that test.
(A list of the various tests can be found here if you're curious.)
To increase the score for a particular test, log into cPanel and click the SpamAssassin icon, then click the Configure SpamAssassin button at the bottom of the page. On the configuration page you'll see the required_score value, which by default is 5 but can be adjusted if you wish. Following this is a section with rows of fields with the word "score" out to the left of them. Unfortunately this section is not very well documented within cPanel, but it's fairly easy to use.
In one of the fields, enter the name of the test, (the upper case test identifier from the header), followed by a space and the new score.
For example, if you see that the test RCVD_IN_SBL, which indicates the IP of the sender was found in the Spamhaus SBL blacklist, contributed 1 point to the score, but the overall score only reached 3, the message needed another 2 points added to the score to be considered spam, so you might boos the scoring for RCVD_IN_SBL to 3. (This is a very simple example, you really should examine many headers and try to find some common tests that are involved in many of them to find a good candidate for a higher score.)
To change the scoring for RCVD_IN_SBL from the default 1 to 3, simple enter this in one of the score fields:
Once you've saved, you'll see that in the list of scores, instead of just score followed by a blank field, you'll see "score RCVD_IN_SBL" followed by 3 in the field. You now have an overridden score for RCVD_IN_SBL that you can adjust further by simply changing the 3 to a new value.