For a while, it was configured to discard spam. Later, I configured it to put the spam in a special IMAP folder. I have the same system today, but on top of that, I have a background shell script that watches my mail folders and runs sa-learn on them. Anything that appears in the spam folder is learned as spam. Anything that appears elsewhere is learned as ham. Most of the time, this will be email that has already been classified correctly, but if I move an email, it will reclassify it.
Some time ago, it began leaking spam into the inbox. It turned out that I needed to make the Bayes scores more aggressive, and after I did that, it's been more or less perfect. More or less zero false positives and maybe a couple of false negatives per week.
I find that the good old Bayes classifier is still the most powerful tool in my spam filtering toolbox. You just have to be persistent and consistent in how you train it and tune it. For example, you shouldn't train it to classify legitimate newsletters as spam even if they are undesirable. Instead, you should unsubscribe and put those in the trash folder. I find that this considerably reduces the false positives.