"Could this also be done as suggested in QB Help when applying upfront payments (carried as liabilities until the work has been performed) to invoices? With this method, instead of using a credit memo, a line item (e.g., Client Phase Payment) with a qty of -1 is added to the invoice along with the amount of the payment. Or, is there a reason it shouldn't be done this way with progress invoicing?"
Here is what happens and why I do not recommend this method:
Every invoice that has any negative on it, this is the Date of that payment, applied to the invoice = Paid on Cash Basis. If that prepayment makes a Partial Payment, this is Partially paid and Weighted allocation. If there is Sales Tax, that also is Partially owed. A $100 sale with 7% sales taxes, that is Half-paid, will = $50/$107 Cash Basis Paid for that date.
You can see this in my attached example.
We don't even have sales tax consideration. Here is another reason I stopped doing this, however:
In Customer Center and in Transaction Listing reports, you will see the Transaction as a row with its amount. Example: If you get prepayment and the invoice has that as negative, your Transaction List and report will show the invoice amount reduced. Example: $100 invoice with $100 prepayment entered directly on it = $0. Every time you look at that, you need to double-click to Open it to find the Actual Sales amount was $100. It shows as a $100 sale on Sales reports, but in Transaction Listings, the invoice ended as $0. If you use Invoice for $100, and credit memo to make the $100 prepayment available, then in Transaction listings in Customer Center and in reports, you see $100 invoice and $100 credit memo. And now, the clarity of the credit memo existing = I know I applied their prepayment, because that is why I use Credit Memos; and now you Also get to put a Date on the Credit Memo to apply their prepayment and control this for "partially paid by prepayment" to avoid the Cash Basis weighted allocation as the Invoice date.