Just posting this because so many other articles online seem out of date when I was searching for this issue.

With the ‘old’ version of Google Analytics, you could only have a 1:1 relationship between Adwords and Analytics accounts, so if you maintained multiple analytics accounts you would need to set up multiple adwords accounts, or manually create tracking URLs and deal with the lack of auto-tagging data.

The new version of Analytics allows you to link multiple adwords accounts to Google analytics, and this blog post tells you how!