This documentation is for Taxamo v1. If your account is with Taxamo v2 use the documentation at integrate.taxamo.com/doc.
If you are uncertain of your version please contact support@taxamo.com for assistance.

How should I configure the PayPal IPN URL for subscriptions with Taxamo if I also need the IPN URL linked to my website?

This is a known limitation of PayPal. The best thing to do is to handle that webhook on your end, and then just forward that same message to: https://api.taxamo.com/app/v1/webhooks/paypal?public_token=your_public_token

Here are links to example solutions, and more information. Please note that these solutions are neither supported, nor endorsed, by Taxamo: