Creating two colour prints

I’ve been experimenting with trying to design objects for two colour printing, but finding it a bit tricky. I was able to successfully get the Vertex bracelet to print and I’ve been able to use dual extruders to print supports and models with different materials but when I try to create my own objects, I’m running into problems. I’m quite new to 3D design so it may be that I’m just missing something really obvious.

Using Autodesk 123D, I tried to create something really really simple as a test. I created a 2cm square cube, and then cut out a 1cm deep 1cm radius circle in the middle. I then put a 0.9cm radius cylinder 0.9cm high into the middle of it, so the circle sits perfectly inside the cube and does not overlap it at any point. I exported it as an STL, then loaded it into Repetier. Repetier allows me to split up the object and assign different extruders to the cube and the cylinder, but it loses the Z height information, so the cylinder now sinks down inside the cube instead of sitting in the space intended for it. This happens with everything I’ve tried - the X and Y positions are perfect but the Z heights always get reset.

I tried to find some tutorials but all the ones I found use a different method of exporting the objects as multiple STL files. While I can get this to work, it also loses all the information on the position of the parts relative to each other as Repetier will try to auto position them when the STL is imported.

If anyone can suggest anything or point me to any internet resources I’d be grateful.

In the Repentier software you need to drag them in the same object group, so that it understands they are part of the same object.

These instructions explain the entire process pretty well: