To track your Paypal Customers payments you can either set up a clearing account or use the undeposited funds feature within QB using your bank account and deduct the fees on each deposit.
When post the payment to the Customer, post the full amount. When you make the Deposit, enter a line under the payment and in the From Account drop down enter the account you wish to post the fees to and enter the amount as a negative.
If you do not have fees that you want to post to specific payments you may want to just set up a clearing account.
To set up a clearing account so that you can track your Paypal account just as you would a bank account:
Set up a Contra (clearing) Account.
1. Go to Lists>Chart of Accounts and right click on any account
2. Choose New and choose Bank for the type
3. You can name it whatever makes sense to you such as Clearing Bank Account, Paypal Account, etc
4. Use this account to post to for both transactions, Income and Expense and they will zero out the account and no Income or Expense will be realized.
In this case you would set up the Account and post the Customer payments,
then "write a check" for the fees and post to an expense account for the fees
and when you need to post a deposit to your bank account either go to Banking>Transfer funds or "write a check" to the bank account.
If you use the account for purchases you would just "write" a check in QB. You can also use the QB Banking>Transfer Funds if you transfer funds from this account to one of your bank accounts.
If you want to download the transactions
http://support.quickbooks.intuit.com/support/Articles/HOW12746
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