I'm looking to print a shelled shape with a 2nd colour inner but can't work out how to programme Slic3r to do this - if I try to build an .amf file from separate .stl ones it automatically assumes the inner begins at the same level as the base of the shelled object. Is there a way of setting a Z offset for the 2nd .stl so that it sits on top of the inside of the shelled object?

Yes, with your second object selected, click "move object button" in the right panel and then you can place your x,y,z coordinate´s model. Fisrtable you can see the another model´s Zmax in the object properties panel, to place correctly the origin of your second model.

Sorry for my bad English.