In order to use our version of the GA tracking code, you must be using our standard Add to Cart and View Cart button codes that display the cart as an overlay "inside" your own page. Make sure every page that has any number of Add to Cart buttons also has one complete block of your View Cart code, which loads some javascript into your page for managing the overlay-style cart display as part of that page. Also, make sure you use only our version of the GA tracking code in every page where you want to use any GA tracking at all -- i.e., do not mix'n'match our GA code on some pages with Google's own GA code in the same or other pages.
However, if you prefer to use any standard GA tracking code as provided/documented by Google (including Google Website Optimizer), you should use only that code on all pages (instead of using our version of the GA code), and add that code to your E-junkie-generated thank-you pages as explained here:
http://www.e-junkie.com/ej/help.custom.thankyou-page.htm
See also the tips on conversion tracking covered here:
http://www.e-junkie.com/ej/tips.tracking.conversions.htm
Finally, bear in mind that browser settings/extensions which affect cookies or javascript can interfere with Analytics-style tracking, which is therefore mostly only useful as a relative metric for more/less and before/after types of comparison, rather than an absolute precision-headcount metric. Across a large enough number of visitors, the variables of cookie/javascript blocking will be a fairly consistent factor regardless of any variables you control in your site or marketing. Even though the numbers are not precise, the degree of imprecision or "margin of error" will be fairly consistent, so you can compare when changes to your site or marketing efforts result in significantly more or less traffic or conversions than before, or when more or less traffic and conversions appear to come through one part of your site vs. another.