If you want to send credit card transactions to the paypal gateway and stay on your website you have two main choices, Payflow Pro and Website Payments Pro. Payflow Pro is a payment gateway solution that can be used with any Internet Merchant Account to process credit card transactions. If you are using Payflow Pro with PayPal as your Internet Merchant Account to process credit card transactions online then you should use Website Payments Pro.
The confusion is about the merchant account that you have signed up for or wish to use. If you have Paypal as the merchant account, then you would use the website payments pro payflow edition, which is API based from your website and shopping cart. The Website Payments Pro gateway uses a sandbox account and your website/cart submits to the sandbox to process the account.
If you have a 3rd party merchant account with a bank like Wells Fargo then you need the Payflow Pro gateway. Our client we integrated had a merchant account with another bank. Payflow pro doesn’t use a DLL with an API. You pass the data in XML or name-value pairs to the server along with the login credentials. This link on the paypal website explains the differences.