Hey Mick101,
It sounds like you're running into a situation where payroll expenses are being doubled due to both the automatic transaction created by the pay run and the bank feeds for net payments and PAYG amounts. To prevent the double entries in the future, when you create a pay run transaction, you'll need to match the bank feed for the net payment rather than allocating it as this will create another transaction.
To correct the double entries you already have, you can check the Find Transactions window and delete the duplicate transactions from there. Make sure to check the links below for more info.
Cheers,
Doreen