I'm having trouble with SpamAssassin and amavisd-new.

Your first port of call – even before reading the SpamAssassin FrequentlyAskedQuestions list – should be the amavisd FAQ list.

Amavisd intercepts configuration settings, so a lot of the SpamAssassin documented ways to set configuration work slightly differently under amavisd. It's very important that you understand what amavisd does in these case, so be sure to read that product's documentation and FAQ before asking questions about SA.