Using rafts with DualExtrusion prints

Question: I have a Grid II Dual, and I’m still trying to get familiar with printing dual colors in a single print. If I wish to add a raft when printing dual extrusions do I just add it for one of the STL files windows that appears after I click on "Merge Stl for DualExtrusion? And if I do it this way, do I then need to somehow compensate for the change in the starting height of the actual part in the other STL file? Seems that if I add a raft for both STL files the rafts will overlap.

why not use Mprint ,it’s more convenient for dual color printing http://www.mbot3d.com/software
here is a video about it https://drive.google.com/file/d/0BxAApICl23VCd2x0cU1YenFseTA/view?usp=sharing

I’ll consider using Mprint. But I still have the same question regarding printing with rafts. Can I use rafts when running a dual extrusion print?

if you are using Mprint ,yes ,you can print the raft