If you're an IDEA user, by far the best way is to use SBT to manage your projects and use its sbt-idea plug-in (which adds the gen-idea
task) to create IDEA projects files and directories.
Ideally, use Paul Phillips' SBT launcher (to get SBT version flexibility if you're ever going to build 3rd-party projects whose specified SBT versions can be all over the map) and configure non-project-specific plugins, such as sbt-idea, in your per-user shared ~/.sbt
directory. That way all your projects have it automatically yet it does not intrude on the project definition itself.
Optionally, there is an IDEA plug-in that integrates SBT's interactive console with the IDEA app. The best part of that is compilation errors become hyperlinks to your code.
I don't know if there's an Eclipse counterpart to sbt-idea, but even if there's not, SBT is the way to go.