Let me help you record the payment.
First off, you'll need to set up a clearing account. This will be used to move money from one bank to another since the payment was processed by a different payroll company. Here's how:
Next, add the third party company as a vendor and write check to record the transaction they made through direct deposit. See the steps below:
Once done, you can pay the vendor bill using the clearing account. Here’s how:
I've attached screenshots below for your reference.
Please feel free to leave a comment below if you have any other concerns.