Build the ships separate then save them as sub-assemblies (there's a green tab in your parts section in the VAB and SPH). Make sure to use the root function to make the root part something that can attach to other stuff: like a decoupler or a docking port. Then just load the rocket and go to the sub-assembly tab and grab your previously made 2 ships and attach how you like. Easy-peasy...done it a few times myself.
netbumbler's post in Has anyone tried this?? was marked as the answer