Generally payments against invoices from PayPal are treated just like cash or check payments, except instead of depositing them into your regular bank account, deposit them into your PayPal bank account in QuickBooks.
PayPal functions like a bank accounts, and so set it up that way in QuickBooks. Then deposit the payments to the PayPal account. Later, when you transfer money from your PayPal account to you regular bank accounts, create a transfer to move the money.
