I want to get a SSL Certificate for my domain, but I'm worried about something. Because I use a third party for payments(paypal), when they leave my page to go pay, would it tell them that they are leaving my certificate, and then tell them another certificate is being accepted? wouldn't that make them worry as to not know which certificate to trust and such?
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I don't think Paypal uses self-signed certificates, it should already be in the customer's root store. AFAIK, SSL<->SSL is a smooth transition, just make sure they have already accepted your SSL Certificate from your site.