If you are using E-junkie with Zencart, then you would not be using any of Zencart's own built-in cart/payment/eCommerce features. Essentially you would be using Zencart only as a CMS to build a templated site and manage your product listings, so you would be pasting your E-junkie cart button HTML codes into the product description section for each product.
As such, you should not need to configure any PayPal Pro settings regarding Zencart's settings. For E-junkie settings, please review our PayPal Pro integration procedure here:
http://www.e-junkie.com/ej/paypal-partner.htm