I agree with Mullhollander. Start with the cantonal business development agency of the canton (s) in which you are interested in setting up shop. These people have the job of attracting foreign companies to their specific canton as well as answering (for free) all of your questions about setting up with the specific situation you have (non EU, sub vs. HQ, permits etc.).
However (this is the main point), the level of interest varies dramatically from canton to canton. For example, Vaud is very active. I am less sure of the Swiss German cantons where there is a much larger industrial/economic base already.
You can find the details on each canton's agency with a quick Google search. You will get 90% of your questions answered in a one hour one-on-one meeting. Then you will have some facts to work with.
P.S. The cantons handle most of the permit allocations hence they are the ones who can tell you how things really work.