1. Create an Invoice Item in Settings and label it however you want your retainer to be labeled within the Billing and Expenses tab (Red Arrow).  You will also need to set the Unit as "Each" (Blue Arrow), it needs to be set to "each" because the retainer could be a different value every time. Once the above has been submitted select submit.  

2. When creating a case file instead of entering the amount of hours as budget add the amount given on the initial retainer. 

3. Once the budget is set go to the "Billing and Expenses" tab and click "Add Invoice Item". In the pop up window select the date the retainer is received and then pick "Retainer" as the invoice item (Red Arrow). Select 1 as the Quantity of Invoice Item (Blue Arrow). Then in the cost field enter the retainer amount and put a negative in front (for this example I have a $2000.00 retainer)(Green Arrow). A description can be added but it is not a required field. Once done hit submit. 

4. At the end of your case you will add the other invoice items the normal way when there isn't a retainer and you select all services plus the retainer. The invoice will show all of the services/investigative hours (red arrow) going against the retainer. If the subtotal (blue arrow) is negative that shows how much of the original retainer is left. If the subtotal is positive that is how much the client owes you after the retainer.