Fees that are deducted from your QuickBooks Payments transactions are automatically recorded into QuickBooks Online once you have connected the accounts. Here's how you connect your QuickBooks Payments account to your QuickBooks Online account:

  1. Select the Gear Icon on the top > Company Settings/Account and Settings.
  2. Select the Payments tab.
  3. If you already have an account, click Connect. If you don't have an account yet and want to sign up, click Learn More. 

After doing this, you'll be able to select the Expense account you want to use to track QuickBooks Payments feeds in for reporting purposes. Here's how you can change that:

  1. Connect your QuickBooks Payments account.
  2. Select the Gear Icon on the top > Company Settings/Account and Settings.
  3. Select the Payments tab.
  4. Change the Expense in the drop menu next to Where should we record Payments fees?

Payments Fees Account setting

Note: Make sure the deposit account above that is selected as the same account you actually receive your deposits and fees deducted from in real life. That account can be changed by accessing the Merchant Service Center, which you can get to by clicking Manage Details

If you are using the Downloaded Transactions feature to connect to your bank, you'll notice the batches will automatically be Matched. This is because any of your payments will automatically go into the Undeposited Funds account in QuickBooks Online as soon as you process them. Once they settle and are deposited into your checking account in real life, the batch will automatically record (with the fees deducted out of the batch) in QuickBooks Online and you can match it on the Transactions>Banking page.