I did some further testing, and it seems if I use any account other than A/R to record the resolving lines on the bank matching page, then amounts don't properly tabulate on the customer's detail page. If I use A/R and the customer's name on the resolving line, then an expense gets created in the customer's name. I can then visit the customer's page, pull up that previous payment amount and check-off that expense to resolve the initial overpayment.
As a concrete example:
Store A invoice #101 is $100
Store B invoice #102 is $100
Store C invoice #103 is $200
First week deposit is for $300, which I record as $200 (overpayment) for #101, and $100 for #102. This creates a $100 credit for Store A.
Second week deposit is for $100, which I record as $200 for #103, and add a resolving line for -$100 against A/R in Store A's name. This creates an expense in Store A's name.
Then when I visit Store A's customer page, I can see $0 open transactions, but $100 overdue. If I then click on the auto-generated payment from the "first week" deposit, I can revise the matches that already include invoice #101 and now also check off the box next to the auto-generated expense, and the totals match up.
The customer's page now shows $0 open and $0 overdue correctly.