Hi willowpitch,
Thanks for joining us here on the Community.
The recommended way to do this would be to post the sales receipt with the total sale amount to the 'Undeposited funds' account, and create a Bank Deposit after this to account for the fee.
To create the Bank Deposit:
1) Select New > Bank Deposit
2) Tick the sales receipt showing under 'select the payments included in this deposit'
2) Scroll down to 'Add funds to this deposit' and change the 'VAT amounts are' drop-down to 'No VAT'
3) On the first line under 'Account' select the PayPal fee or expense account you wish to use to track the fees and enter the amount as a minus figure (-)
4) The bank deposit should now total the payment that you received - save & close and match this in the banking
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