We sell physical books, that are sent via the mail. We also sell digital downloads, that are obviously not actually 'sent'. Books carry a shipping charge, per order. That is, not 'per book'. Downloads don't (and get managed through a third-party download service - though the payments happen through our Paypal account). However, the way we've got things set up we can't see a way to accommodate this arrangement. If we set shipping as part of the button, then shipping is aggregated/multiplied for each book. If we set shipping as an overall 'per order' charge, then downloads get charged it, incorrectly. Would very much appreciate some assistance. We are not 'developers' so please, simple explanations! Thank you.
I recently had a similar issue come up. Your best solution might be to create a separate PayPal account; I don't think there is much you can do about the shipping miscalculations.