If the origins aren't set properly then the slicer isn't going to know where they should align, surely?
If you're lucky and they have a common face then you could try aligning but setting that face on the bed on each, but other than that you're a little stuck for it to be done automatically, I imagine.
I assume that these aren't bodies you designed yourself? If they are, then your best option would be to properly align them in the CAD package before exporting. That way the origins will be set properly and S3D will be able to snap them together properly