Thomas,
Method out of the box does not apply "credits" against invoices. this left best to QB...
But There are several other approaches that would work in Method and the ones I like best are...
Generate an invoice for the "deposit" using an Item that points to a deposit or something like that. And then Receive payment against that. When the work is done, genrate an incoice for the amount owed and then add a new line showing using a negative "deposit item" on that invoice to zero it out..
Or you can Receive Payment and do not apply it to an Invoice. Then when work is done, generate work invoice. Go back to Receive Payment and apply to new invoice.
Just some ideas.