Fixing it with a single journal entry isn't possible because QuickBooks only allows one A/R or A/P account per journal entry.  So you'll have to enter separate journal entries for each customer.  Worse, using journal entries will actually cause more work because you’ll have to go back into each payment to apply it to the journal entry you created.  Since you have to do them one at a time anyway, it’s much easier to just create the invoice and apply the credit right on the invoice. 

But more importantly, QuickBooks works much better with transactions.  For instance, journal entries aren’t going to show up on your sales reports because they’re based on sales items and you can’t enter items on journal entries.  Of course, you can modify your reports to include them but now you've introduced unnecessary complexity to the fiie.   

For this reason, I recommend avoiding journal entries unless absolutely necessary and never ever using them to replace a transaction.  They should be limited only to non-transactional entries, like depreciation or prepaid expenses, and even then if you are doing job costing you’ll need to do a $0 transaction instead because most of the job costing reports are based on items.