I figured out my issue after watching this video from Google I/O 2013 which is using Android Studio, but it was the same thing as Eclipse mostly.
My mistake in following https://developers.google.com/eclipse/docs/endpoints-addentities was that you need to put your entity class into the MyApp-AppEngine project and NOT your MyApp project.
That was the source of confusion. In case it helps those in the future, here is a short breakdown of what I did.
- Put the Entity class you want to add to App Engine into your MyApp-AppEngine project.
- Right click your class and go to Google > Generate Cloud Endpoint Client Library
- Right click your MyApp-AppEngine project and go to Google > Generate Cloud Enpoint Client Library
- New references will be made in your MyApp project which you reference in your project for usage.