This is our main help page for Tracking integration with Google Analytics (the other pages linked above cover more specific tracking-related concerns and scenarios in detail):
http://www.e-junkie.com/ej/help.tracking.htm
If you use our version of the Google Analytics (GA) tracking code, we would recommend just using your standard E-junkie-generated thank-you pages, as this will be the least complicated approach and allow us to add Ecommerce Tracking details in those pages for GA to pick up. In this case, you would just leave your Common Thank-you Page URL setting blank.
If you wish to use Goals-based conversion tracking, the help page I linked above has a section explaining how to set that up, including the Goal URL and Match Type you should specify in your GA account if you're using our standard thank-you pages.