Please Learn from this input. You have it Backwards. When a customer Pays, you use Receive Payment. That flows to the bank account directly or is grouped into UF. That's when you use Make Deposit.
You don't jump to Make Deposit and put AR there. You overlooked the entire Receive Payment function for processing a customer payment is the First Step, not later.
Let's review that this is both a vendor relationship and a customer relationship.
The Vendor Name has to have Gross Paid to them on the check details, even though the Banking will be Net. That's because of the Required reporting as 1099-Misc.
"It will either be automatically deducted from their commission check"
This is Barter. Make a Bank account and name it Barter.
Use Write Check to John Jones (Vendor). List the Gross or Full Commission owed to them. Now you are ready to Receive The Payment, for the amount their Customer Name version owes you against the invoice for charges. Deposit this to Barter Bank.
You see the Difference here is what you owe them, in reality. In the real checking account, "Write Check" to their Vendor Name and on the expenses tab, enter the Barter Bank and pay them this Balance.
Now the Barter Bank = 0.
"or if they can write a separate check."
This is just like any Customer Payment = Customers menu > Receive Payment. Apply it to the open invoice.