When ATP is enabled, all your Custom configurations (profiles, policies, etc.) will still be there and available if you switch ATP back off. The biggest thing for enabling ATP is to make sure all your exceptions are GLOBAL and not attached to rules as the latter will suddenly stop working when ATP is enabled which can be a rude shock.
Here are the pages from my IPS/AV/ABOT Immersion class covering this tip and some other gotchas, only update to this would be the new SK covering how to customize UserChecks while ATP is enabled: sk178764: How to use a custom UserCheck object for Threat Extraction in the Autonomous Threat Preven...
Gateway Performance Optimization R81.20 Course
now available at maxpowerfirewalls.com