You can achieve this, for example, by adding something like the following to your build.sbt :
unmanagedSourceDirectories in Compile <++= baseDirectory { base => Seq( base / "some/subdir/src" ) }
For more information on the relationship between unmanaged-sources , unmanaged-source-directories and scala-source you can check the documentation. After exporting the eclipse project from sbt, you should find the corresponding entry in your .classpath file, for example:
<classpathentry output="target/scala-2.9.1/classes" path="some/subdir/src" kind="src"></classpathentry>
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