If you want to apply the Retainer while you are making an Invoice, there is a box at the bottom of the New Invoice window where you can enter the amount of the retainer that you wish to apply. (See the blue text in the Retainer Box at the bottom of the screen shot below)
If you want to apply the Retainer to an Invoice that you have already accepted or to an existing Proposal as a deposit, then you need to go into the New Cash Receipt Window and do the following:
- Leave the amount at the top at 0.00
- Tag the Retainer line and click the Edit button on the right hand side
- Enter a NEGATIVE amount for the amount that you wish to apply to this Invoice and click Ok
- You should see this negative amount come up in the last column of the Retainer line called "This Payment"
- Next Tag the Invoice or Proposal that you wish to apply this money to and click the Edit button on the right hand side
- Put in the same amount as you put on the Retainer line, but make it POSITIVE and click Ok
- You should see this positive amount come up in the last column of the Invoice line called "This Payment"
- At the bottom of the window you should see the box Total Dep/Ret with the negative amount and the Total Payment box with the positive amount and the Total Receipt box and Difference should have a 0.00 amount
- Click Ok and post the combination of receipts.
See the screen shot below as an example of the application of $133.65 of a $2,000 Retainer to an Invoice.
See more detailed steps here.