Hi Baphs,
A bit more information would be great but for a starting point you could read the article below:
Did you setup a current bank account? If not you should do so. When paypal transfers your money from your paypal account to your current bank account you write this as an new transaction (money in) in your current bank account and tag it as an bank transfer from your paypal account you already have created. If you have auto feed for your current account as well you don’t need to write a new transaction the auto feed will create this transaction over night for you and on the next day you just tag it as an bank transfer from your paypal account.
If you get paid over paypal you create an invoice in quickfile and tag it to the transaction in your paypal account (in quickfile). You can also tag/create the invoice from the tagging button inside your paypal account (in quickfile). For the fee paypal charge you, which is also uploaded to your paypal statement (in quickfile), you create/tag an purchase invoice with paypal as the recipient.
As a tip: In your paypal account settings in quickfile you can find an option to ignore an upload of your payout transaction (from paypal to your current account) which you may tick. Because of the way quickfile works it is very likely that you will end up with 2 entries which is a bit confusing at the beginning.
I hope it helps a bit.
You can find quite a lot of information in the quickfile knowledge base