Within a Client Invoice, under the Receipts tab, there is a sub-tab called Prepayments. This guide describes its use in the system.
The typical example of when Prepayments would be used is when a client sends you money for no apparent reason (no client invoice has been generated, nor is this an advance bill).
With the above example, you would create the receipt in Workamajig and post it. This posts to the Unapplied GL Account by default for that period.
Next month you create the client invoice. In the Prepayment tab, you can now apply that unapplied receipt against this new invoice. Post the invoice. Which then accounts for next months financials and reverses out the unapplied amount.
NOTE: Normally, you would create the Client Invoice first, post it, and send that to the client. Then once you receive the client payment, you enter that as a Receipt and apply it to the existing invoice.