Hello there, Jw11.

You're unable to merge 2 customers to one parent account (customer). You can only merge 2 customers to each other and all transactions will transfer to the customer you will retain. 

I have a suggestion so you apply one payment to multiple customers. You can use our bank feeds feature. Once you set it up, you can match/apply the downloaded transaction (payment) to multiple invoices. Here's how:

1. Click Banking.
2. Go to Bank Feeds, then choose Bank Feeds Center.
3. Choose the bank account, then click Transaction List.
4. Choose the payment.
5. Click the Select drop-down arrow, then choose Add More Details. 
6. Choose the payments in the Undeposited Funds tab, or choose the invoices in the Open Invoices tab.
7. Click Add to QuickBooks.

I've got you an article for more information: Add and match Bank Feed transactions.

Let us know if you have more questions. We'd be happy to answer them.