http://zqktlwk5ilgohy63eyrptyb4mc76bunfmxcnstkmveyjnskxkpq3b5yd.onion/wiki/Anonymous_Communications
The instructions are a little confusing, but basically you want to edit your preferences to tell Azureus that your tracker server's external IP is your .onion address from Tor. So long as the port here matches the public port in your tor hidden service config, you should then be able to give people the .onion address.