You'll want to set up a deposit or retainer process for your company. There are several steps in taking account of that money. You may need to set up a current liability account for upfront deposits, and retainers are liabilities, though you deposit the money into your bank account.
Here's how to create a liability account:
Go to the Lists menu, select Chart of Accounts.
In the Chart of Accounts window, right-click and select New from the pop-up menu.
Select Other Current Liability as to the account Type.
Enter a name for the account (for example, Upfront Deposit) in the Name field.
Once done, you need to create an item and use it when recording upfront deposits or retainer. You can check out manage upfront deposits or retainers and go directly to Step 2 for the detailed steps.