It may be recommended but not strictly necessary to put FB's tracking code in the HEAD of your thank-you pages; if it can work in the BODY, you could just put that in your Account Preferences > Common Thank-you Page HTML (which would be inserted once near the end of every thank-you page we generate for you), or in the "Message (HTML)" field of the product's settings (which would be inserted after the name of that product only on thank-you pages we generate for orders of that item).
If the FB tracking code really must be in the HEAD for some reason, I think this help page may be relevant for what you're trying to accomplish:
Note that Google AdWords tracking is (or can be) separate from Google Analytics tracking; if all you really need is conversion tracking for AdWords, you can simply paste your AdWords tracking code into your thank-you page, whether you're redirecting to a page on your site or using your standard E-junkie-generated thank-you pages.
If you will be using our custom version of the Google Analytics tracking code, you would need to use that version of the code on every page where you want GA tracking, including the thank-you page on your site (the latter is not necessary if you're using standard E-junkie-generated thank-you pages). Our version of GA tracking code is documented here: