When you pay with Paypal, sometimes the balance is not enough to cover the entire amount of the transaction. In this case, Paypal will automatically transfer the needed difference from your linked checking account. To record the payment in CustomBooks™, use Paypal as the method of payment and the account and then a transfer can be created to record the movement of the difference.
If both accounts are in Cloud Banking, you can match the Paypal transaction to the bill, and then record the difference by choosing match in the transfer transaction.