To create an advance deposit:
Go to Accounts Receivable > Payment Processing
Click on one of the batches and then click on Enter Payments button or create a New batch.
In the Payment Processing window, choose a customer and enter an amount into the Amount field
Open Other tab
When in the Other tab, mark the box for Advance Deposit and then select the Job you want to apply it to. Then save.
Once the Advance Deposit is created, it will be available to the job. You will see this as a credit on the customer labeled as credit type ADVDEP.
When the job is invoiced, you should see the advance deposit on the job invoice or you can unmark the Use Adv Dep box in order to apply the advance deposit to another invoice on the job.