We can't speak to initial enrollment issues at PayPal's end such as SNS described, but once you're properly enrolled for PayPal Advanced with them, you'd just follow our instructions to configure settings in your PayPal Manager and E-junkie accounts:
The last step there links to a setup form at our end, where you'd enter your PayPal Manager credentials; submitting that form would disable PayPal Pro and enable PayPal Advanced for your E-junkie Cart, which should take effect instantly, no need to change your existing Cart buttons or anything like that.
One issue we sometimes see is with the Transaction Password credential, which needs to be 6-16 characters long, alphanumeric (letters and numbers) only. PayPal Manager allows setting a Transaction Password up to 32 characters long, but their documentation for Advanced was inconsistent about that (some places said 16 char. max., others said 32), so we went with the more conservative limit to be on the safe side. We'll be reviewing PayPal's current documentation to see if they've resolved that inconsistency; meanwhile, stick with the 16 char. max.
Functionally speaking, the only significant benefit of Pro is access to a Virtual Terminal for charging offline card payments (e.g., for orders placed by phone, mail, fax or in-person); if you don't need that, Advanced would probably be sufficient for your needs. Any custom/third-party Integration you'd set up in your E-junkie account settings, to have us forward order details to a script after we process an order, would continue working just the same as before if you switch from PayPal Pro to Advanced.
The checkout flows for buyers differ slightly as well; Pro has the buyer enter their card details on the same page where they enter their Billing/Shipping address (a secure page we manage for you), whereas Advanced has the buyer enter their address(es) on our secure page and then proceed to another page (hosted by PayPal) to enter their card details. You can compare the checkout flows on our Pro and Advanced demo pages: