The sbt-idea plugin works with multi-module sbt project. We have been using it since somewhere around sbt-0.10.0, and currently are at sbt-0.11.2. It seems like you have the dependency part of the build file set up ok, so here's an example of how we do the project setup from a full specification Build.scala file:
object Vcaf extends Build {
import Resolvers._
import Dependencies._
import BuildSettings._
lazy val vcafDb = Project(
id = "vcaf-db",
base = file("./vcaf-db"),
dependencies = Seq(),
settings = buildSettings ++ /* proguard */ SbtOneJar.oneJarSettings ++ Seq(libraryDependencies := dbDeps, resolvers := cseResolvers)
)
lazy val vcaf = Project(
"vcaf",
file("."),
dependencies = Seq(vcafDb),
aggregate = Seq(vcafDb),
settings = buildSettings ++ Seq(libraryDependencies := vcafDeps, resolvers := cseResolvers) ++ webSettings
)
}
In the example, the vcaf-db project is in the a folder within the vcaf project folder. The vcaf-db project does not have it's own build.sbt or Build.scala file. You'll notice that we are specifying libraryDependencies for each project, which may or may not be your missing link.
As ChrisJamesC mentioned, you need to do a "reload" from within SBT (or exit sbt and come back in) to pick up changes to your build definition. After the project is reloaded, you should be able to do a "gen-idea no-classifiers no-sbt-classifiers" and get an intellij project that has the main project, modules, and library access as defined in the build file.
Hope it helps!