I'd highly recommend leaving the IDE and diving into the sbt world for developing Scala apps (esp. with Scala/Android). I've been developing a pet project some time ago, it uses proguard and the config is embedded in the Build.scala there, you can have a look at: https://github.com/ktoso/kanbanery-tv/blob/master/project/Build.scala
Other than that you'll want to read up about the latest version of: https://github.com/jberkel/android-plugin (or join the mailing lists mentioned there where all the scala+android people hang out.)