Assuming you have define your flavors like this:
productFlavors {
flavor1 {
...
}
flavor2 {
...
}
}
You can modify the sourceSets of each flavor
android.sourceSets.flavor1 {
java.srcDirs = ['src_flavor1']
resources.srcDir = ['res_flavor1']
}
android.sourceSets.flavor2 {
java.srcDirs = ['src_flavor2']
resources.srcDir = ['res_flavor2']
}
I hope this help... (don't hesitate to add more details about your problems since it will help us to help you)
Last remark: according my experience, Android-Studio is not very stable yet and not full-featured yet regarding gradle<-->IDE sync. So I strongly suggest you to always test your gradle scripts from the command line.