Theoretically upgrading from 0.4.x to 0.6.x is as easy as putting the files somewhere, copy the config files over, and start the bot.
For custom modules you might have to do some adaptions. Or I think there still is a 0.4 support module around, written by Temar. For many modules this one will enable you to work with your old module versions. Or if you are lucky someone else will already have done the needed work.
One small warning: there is no automatic way to revoke the db changes from 0.4 to 0.6. So if you want to be able to go back make a db backup.