In order to move funds (money) from one Document or from Retainer to another Document, you will need to use the Cash Receipt window.
In both Standard and Pro the Cash receipt window is similar.
There are many different situations that can be completed; from moving a deposit from one Proposal to another, or to an Invoice; as well as moving a retainer to pay deposit on proposal or an invoice; you can also use these steps to use a credit invoice to pay another invoice.
In ALL cases you will use the New Cash Receipt window.
When moving funds, the Amount field at the very top left is always left at $0.00 because you are not receiving any new cash, just reallocating the cash received.
You will Highlight the Retainer line or the Document that you wish to REMOVE the funds from.
Once highlighted, choose the Edit button 
The following window will appear.
In this Amount field, enter the Amount that you wish to remove from this Document or Retainer. This amount should be entered as a NEGATIVE.
Choose OK.
In this example, we will move $481.53 from Retainer to pay Invoice # 10006 in full.
Next Tag & Highlight the Invoice or Proposal you wish the money to be transferred to and choose the Edit button again 
If you are not paying the total due, enter the Positive amount to give to this Document.
Once both Documents have the proper This Payment amount � be sure they are both tagged on the Left-hand side.
As long as the Difference field at the bottom is 0.00, then you can Choose OK to move the funds. *Pro Users will need to post the receipt before it will appear as a payment.
You can Reprint the Document that received the funds and Show the Deposit/Payment in order to see the new Balance.
Below is an Example of moving funds from an Invoice that the Client overpaid or was created as a credit/refund.
In the example below, each payment for Invoice was edited to make the This Payment amounts reflect the amount to transfer/apply.
Invoice #10007 will receive the funds from #10008 and when Invoice #10007 is reprinted � showing payments � this Invoice will now have a Balance Due of $1,357.94. Invoice 10008 will be closed/completed.
In the Example below we are moving a Total of $253.47 out of our Retainer to pay towards deposit on Proposal 0003
We Edited the Retainer line to change the Amount of This Payment to $-253.47
Once both are Tagged, the Difference at the bottom shows as 0.00 and we can Choose OK to process the transfer.
The Retainer will now have 0 Available and the Proposal will have the Deposit entered against it.
***In the Professional version, you will need to POST these Cash Receipts, before the transfers are made.