In Receive Money screen, you can enter the amount PayPal is taking under the Discount column. However, the Discount Account, located at the bottom left of your receive money screen will need to be changed to the GL account for your PayPal Discounts each time.  You can change the Discount Account under Maintain Default Customers, but if you do, then any other discounts your customers take other than Pay Pal will need to be changed to the proper GL account when you enter that receipt.

A little/lot confused here.. Customers are not taking discounts.   PayPal and Square take their piece and leave me with the balance.

I will try this another way.
I record 100.00 received from customer. Square keeps 10.00 and deposits 90.00 to my bank account.
In Sage deposits I show the 100.00 to deposit which is incorrect.
How do I account for the 10.00 deduction in the sage deposit window?

Thanks for the clarification. In the receipt screen you are applying 100% of the customers invoice in the Amount Paid column $100.00, so to reduce the actual amount you received to the bank in the Receipt Amount will show $90.00, I would suggest using the Apply to Revenue Tab and enter the GL account for Pay Pal discount and a minus $10.00 in the Amount column.

Hope that resolves your issue.