I have Eclipse and IntelliJ running side-by-side. I have installed and configured Google Cloud Tools on both of them.
IntelliJ gives me the options to deploy my application to Standard and Flexible App Engine environments. Instructions - https://cloud.google.com/tools/intellij/docs/deploy-flex
Eclipse, on the other hand, only allows me to build and deploy App engine apps to Standard App egnine environment. Instructions - https://cloud.google.com/eclipse/docs/deploying
Is there someway to build an App engine project in Eclipse and deploy it to Flexible App engine environment?
That functionality is under development. You should be able to use the Maven plugins with M2Eclipse in the meantime.