You only want to have certain Matters that will automatically apply trust, not the entire system.
Automatically Apply Trust Account should be checked in System Settings -> Billing -> Posting Invoice.
A Trust account is setup for the Matter. Matter Gear -> Trust
- Navigate to the Billing Tab on a Matter.
- Edit the Billing Settings, Uncheck 'Use Default Settings' and 'Automatically Apply from Trust'
- Press 'Save'.