The correct way to deal with transactions and fees with a payment provider (such as PayPal, GoCardless, World pay etc.) is to account for the transaction in 3 parts:
- The full balance paid into the merchant account on QuickFile (e.g. £100.00), tagged to the client invoice
- The fee paid out, tagged to an invoice for the payment provider (e.g. £5.00)
- The balance which is paid to you, tagged as a transfer between accounts (e.g. £95.00)
There’s a more detailed explanation here which will hopefully help.
As you have several holds, this can cause a bit of a complication. Generally, they can be deleted, and only account for the income once the hold has been released.
You can, to make things easier, record your sales in bulk at the end of a week or month, and tag them to s generic client, such as ‘PayPal Sales’, and account for all the related fees at the same time.
Unfortunately, I’m not able to help with the recommendation, but compare small periods (e.g. a week) from QuickFile to your PayPal account to try and identify the issue. It’s likely to be fees, or even a hold.
I hope that helps!