We're not at all acquainted with Tag Manager in particular, but you can add custom code to your thank-you pages in a few different ways, so you might experiment with these to see if any of them work for your Tag Manager code:
Seller Admin > Account Preferences > Common Thank-you Page HTML:
Whatever you put here would get added at the end of every thank-you page we generate for you, regardless of the item(s) purchased.
Individual product settings > "Message (HTML)" field (relabeled as "Product Thank-you Page HTML" in our new Admin):
Whatever you put here would get added after the product's name in thank-you pages we generate when that particular item is purchased.
This help page provides more detail about customizing your E-junkie-generated thank-you pages:
http://www.e-junkie.com/ej/help.custom.thankyou-page.htm
Seller Admin > Account Preferences > Common Thank-you Page URL:
This would have us redirect all buyers to a custom page on your own site after checkout, so you can build that page however you wish. If you're selling downloads, you can embed your E-junkie-generated thank-you page content (including download links) inside your page with a scripted iframe, as we explain here:
http://www.e-junkie.com/ej/tips.redirection.download-link.htm
