which I imagine that Bayes is learning? Any idea how to 'turn Bayes on'? From what I see, this is constantly updating the files in ~/.spamassassin/bayes_*, but I don't think that spamassassin is utilizing the rules it learned from these files.
Any help clarifying this would be greatly appreciated.
The bayes system must accrue 500 spam, and 500 ham (nonspam) emails in it's learning before it gets used in message scoring.
Via autolearn alone this will take quite some time. It also produces a sub-optimal bayes database (at least a small amount of manual learning is desirable to produce a well balanced bayes db)
I'd recommend getting some emails and feeding them to sa-learn to manually train it... You can get to 500 of each much faster this way, and since you are manually classifying them, you can feed many kinds of spam and ham that SA ordinarily would not autolearn from because it didn't score strongly enough to cross the learning threshold.
