Glad to hear you like the software. What you describe here is a very common scenario in bookkeeping and the way to handle this is to think of the PayPal merchant account as a separate bank account. In your bank management area create a bank account under the Merchant Accounts and Online Payment Services header (just click the grey plus icon).
Create a new bank account and call it something like “PayPal Holding Account”, no sort code or account number required. Now whenever you get paid through this terminal, pay the gross total of this invoice into this new account. Whenever you receive the bulk funds on your current account simply tag these as a payment from the new PayPal holdings account.
Now over time you will see all your sales depositing into the account and the occasional transfer out to your current bank account. The only missing part of the puzzle now is the 2% charge you are paying to PayPal, this should equal the remaining balance on the account, so what you can do is periodically enter a money out transaction on the PayPal account to bring it back to zero then tag that as a payment to a supplier called PayPal Merchant Fees, or something akin to this.
And that is pretty much it! There’s also a similar post here regarding GoCardless…same principle applies.