Similar to the Clojure compiler, you can specify which files are compiled by setting your 'coffeeScriptEntryPoints' in your SBT settings in Build.scala.
For example, if you wanted to not include all files starting with an underscore, add:
coffeescriptEntryPoints <<=(sourceDirectory in Compile)(base => ((base / "assets" ** "*.coffee") --- base / "assets" ** "_*")),
I'm not sure of an easy way to make Play! use a different CoffeeScript compiler though. You might need to do that manually unless someone has an elegant solution.