Unknown said:

is that payment automatically linked to the1200 A/R Control Account in the COA?

Generally yes, but not the way you seem to be describing.

First, if you wish to see how the program will treat an entry, look at the Journal Entry on the Report menu of each data entry screen.  Almost all data entry screens have one.

The A/R control account is the total of all unpaid customer invoices.  If a customer pays an invoice, then you record a receipt that will take that amount out of the control account because it is no longer owing.

If you look at the logic as you do the work, you receive a cheque/payment from a customer, you generally put it in the bank.  So why would the program put it in A/R when you record a receipt, instead of the bank account?  The program tracks reality if you let it (and generally you should let it).