You can. It is in need of updating, but see this:
Basically, just Receive Money => Allocate receipt to Accounts receivable
=> Select customer subaccount => Select Invoice # (or let Manager allocate automatically to oldest invoice.
Your problem seems to be that you created an Accounts receivable
account on your own instead of using the one Manager created automatically when you enabled the Customers
tab. The way to tell which is the one to keep is to go to your chart of accounts and edit the titles of both temporarily to something else. The real one will show Accounts receivable in gray below the edited title. Delete all the transactions to the wrong one and then delete that account. If necessary, recreate the transactions you allocated wrongly. Then you can name the real Accounts receivable
account back to its correct title.