Hole Wizard - 2 Parts

I probably know the answer to this but...

has anyone managed to get the hole wizard to work either in anassembly consisting of a weldment with a sheet cover or just twoparts where one part is a sheet metal box?
The system always seems to want to but 3 parts in top/middle/bottomand hence I end up with a hole in the far side.SolidworksAssemblies