Some trading partners such as Ford, Chrysler, and Visteon make it easy: They will have you use your supplier code as the ISA and GS sender ID.
If your trading partner leaves the choice up to you, I recommend your DUNS number. That seems to be the most commonly used that I've seen.
If you use your DUNS number, the qualifier is 01. If you use something else, the qualifier will vary accordingly.