If you enable Auto-Apply Credits to Newly Created Invoices under your Finance General Settings over-payments will automatically be applied to newly created invoices. NOTE: These are applied to only invoices created for upcoming billing. 

1. Click Setup in the left-hand navigation panel.
2. Click General Settings in the Finance section.

   

3. In the Automated Scheduled Billing section, select Auto-Apply Credits to Newly Created Invoices.
4. Click Done.