I like to use them whenever possible to minimize the number of places I have to look for things. If I'm having a problem, I'll create logged firewall rules and unselect the auto rules while I'm debugging. I have a bunch of inactive "test" rules in my list to be able to do this without changing the rule numbers - keeps the logs consistent with the list. After testing, I re-select the auto rules and deactivate the manually created rules.
Cheers - Bob
Sophos UTM Community Moderator Sophos Certified Architect - UTM Sophos Certified Engineer - XG Gold Solution Partner since 2005