Thanks to Rich Trouton's DefFlounder blog, I was able to find an already existing AutoPkg recipe to create an EndNote X8 pkg for deployment. This was particularly helpful because the install instructions for EndNote X8 are written assuming a user is logged in (not to mention an admin) and the software is distributed with a .app installer (Boo!).
After testing the deployment, I found that the EndNote X8 app still requested activation on first boot. This seemed to be related to the existence of the ~/Library/Preferences/com.ThomsonResearchSoft.EndNote.plist. After a short dig, I found the software looking for the "AcceptedENX7.2EULA". Why it says 7 and not 8 is anyone's guess.
Adding this preference to the global /Library/Preferences folder prevented the additional activation checks and EndNote X8 launched as expected. Ready for the labs!
This is the defaults command we use to ensure activation prompts are dismissed:
defaults write "/Library/Preferences/com.ThomsonResearchSoft.EndNote.plist" "AcceptedENX7.2EULA" -string "1"