Custom Project Layout

Hello, I would like to know how to define custom project Layout. Here is my situation: I have old project:

       ...other javasources

I have created new sourceSets as a solution:

     compileClasspath= sourceSets.main.output+ configurations.myproject
    runtimeClasspath= output+compileClasspath

My problem is with eclipse, I don’t know why I still got errors in markers layout, also what I found crazy that I can compile successfully and gradle generate classes to the destination specified for classesDir . Thank you for your answers