You will need to follow exactly the following steps. You will see MATCH green sign under “New Transactions” section (blue navigation bar on the left > transactions > banking) of bank downloaded deposit (Received) column. In your case for $975.00!

Step#1 Invoice (create + > customers > invoice) for $1,000

Step#2 Receive Payment (create + > customers > receive payment) > select Deposit to: Undeposited Funds account from the drop-down > payment amount = $1,000

Step#3 Bank Deposit (create + > other > bank deposit) >

   “Select Existing Payment” section > amount = $1,000

  “Add New Deposits” section > account = merchant service fees > amount = -$25 (notice negative amount)

Total deposit amount = $975

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Helpful Tutorial Video:
QuickBooks Online: How to record fees from credit cards, paypal, square, merchant processors