how to enable auto-learning & bayesian
 

Anyone knows where the config file is to enable bayesian and auto-learning when using ISPconfig3? the usually spamassassin file is total commented out so can't be that ...

Bayes and autolearning is done by amavis. amavisd strts its own internal instance of spamassassin, so spamd is not used. For details take a look at the amavisd-new documentation, ispconfig uses a default setup of amavisd.