A few things to add:
AdWords is completely independent of Analytics; one doesn't have anything to do with the other. If you have followed our Tracking instructions, added our modified version of the Google Analytics (GA) tracking code to your pages, etc., that would only support Analytics tracking (not AdWords). If you want to put AdWords in your thank-you page, then you'd need to customize your thank-you pages to add the AdWords code.
Note that our version of the GA code would only work if you are using our standard Add to Cart AND View Cart code on every page of your site; if you are not using our View Cart code, or if you are using the non-javascript version of our cart button code, or if you are using our Buy Now buttons instead of cart buttons, then our version of the GA code WILL NOT WORK, so in that case you would need to add the standard GA tracking code to your site AND your E-junkie thank-you pages.
If you are not selling downloads, then there is no reason for buyers to click past the end of checkout to reach the thank-you page, so conversions may not be tracked consistently for those sales. If you are selling downloads, then buyers have an incentive to visit your thank-you page at some point to claim their download, so conversions would track as consistently as possible for those sales. Even so, a conversion will not be tracked at all for buyers who have cookies and/or javascript disabled in their browser.
This FAQ page explains how tracking works in more detail and what factors can interfere with it:
http://www.e-junkie.com/ej/faq.tracking-how-why.htm
