Thank you for your interest in this work. I have an easy answer for your second question: for anything that is a “select multiple” question (see the “type” column of the “survey” sheet in the xls form), you can encode multiple selections as a space-separated list, i.e “1 2” for cigarettes and pipe.
Here is where to look to find out if a question is a “select multiple” in PHMRC_Shortened_Instrument_8_20_2015.xls for when this comes up with other questions:
(This already came up with a different group mapping injuries, see here if you want to know more: https://healthyalgorithms.com/2016/01/28/injuries-query-on-mapping-data-for-smartva-analyze-1-1/ )
In order to answer your first question, I think I need more information. Can you give me an example of what you are trying to do? It also be helpful if you can try it, and let me know what goes wrong if it does not work.