Can someone please explain to me how I set up Paypal integration when my current website (ecommerce site) is already integrated? I can't see how to "add" a second site to my paypal settings, without disrupting my current website payments setup.
Also I want to be able to sell the courses via my own ecommerce site. I understand the thinkific widgets and adding those to my site, but I want people to be able to go through the checkout on my website - as currently people buy courses (as PDF downloads) with other physical (shipped) products in their cart. So I want people to still be able to do this, without having to purchase the course separately. Is this possible?
Yes, unfortunately PayPal allows for only one IPN. It looks like you can do some workarounds for this: http://codeseekah.com/2012/02/11/how-to-setup-multiple-ipn-receivers-in-paypal/
Alternatively, you could choose to take all of your payments through Thinkific or through your own site (linked to Thinkific via Zapier). There's some more info in my other reply to you here.