AdWords tracking is entirely unrelated to Analytics tracking. For AdWords, you would simply need to paste your AdWords code into your own pages and your thank-you page if you wish, although bear in mind buyers may not always view a thank-you page, due to the factors explained at the top of our Tracking help page and in further detail in that Tracking FAQ page.
We are not Google, so there's nothing we can do as you suggest "on the backend" in our system to track conversions any better through Google's own system. That's why Google Checkout is able to send tracking/conversion data to Google E-commerce Tracking consistently, because that's all done within Google's systems entirely at their end, so if complete and consistent conversion tracking is what you require, then you could choose to use only Google Checkout as your sole payment processor and integrate that with Google E-commerce tracking.