How do you mark a bill as paid if paid by your parent company (not by your bank account or credit card)

First, you need to get some guidance from the parent company if they go through inter-company elimination process to prepare consolidated balance sheet report.

In QBO create Intercompany Accounts Payable Account (not main Accounts Payable A/P) >

you can select “Credit Card” Type > it will show as Credit Card group on the Balance Sheet. When you Pay Bills (or enter expenses), you can select this account instead of bank account > easy one step process only > however, if parent company has a problem using Credit Card type account then, you may need to set it up as “Other Current Liabilities” type account.

In that case, it becomes two step process > pay bills (or enter expenses) using Credit Card type as I/C clearing account > transfer the balance from Intercompany Accounts Payable (other current liabilities type) to Intercompany Clearing account (credit card type > new name). To transfer in QBO, you can use Transfer (create + sign > other > transfer) or write a Journal Entry (and make it reversible JE if needed).

Again, it’s a good idea to consult with your parent company who handles Intercompany accounts. And, always reconcile accounts on a regular basis.

Click on the screenshots below to enlarge them
ic payable

ic paybills

ic payable2

transfer

transfer_je

balsheet2
NOTE:
On the parent company’s books, they should record this as an intercompany accounts receivable.
In QBO for Intercompany Accounts Receivable > select “Other Current Assets” Type (not main Accounts Receivable A/R type. In QBO, you can have just one A/R).