Record payments deposits and fees in QuickBooks Online
QuickBooks Online automatically records deposits and fees deducted from your QuickBooks Payments transactions.
Selecting your accounts
Select the Gear icon , then Account and Settings .
Go to the Payments tab.
In the Chart of Accounts section, select the your accounts and save. Note: Make sure the deposit account selected is the same account received payments get deposited to. It should also be the same account where fees are deducted from in real life.
About Batch Deposits
If you are using the Downloaded Transactions feature to connect to your bank, batches will automatically be matched. This is because 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 Deposit will automatically be recorded and a separate fee withdrawal will be automatically recorded in Fees withdrawal account.