The only university I know anything about in Switzerland is the University of Zurich. It is particularly suited if you have interests in behavioural/experiment economics or neuroconomics.
Their application system is pretty simple, you just mail them the required material and that s it. As for tuition fees, they're something ridiculous like 140CHF per semester. However, they do not have funding opportunities. Now you can work as research.teaching assistant, this information can be found here: UZH Financing Opportunities.
They run two different types of programme: Track B, which is the regular PhD, and Track C, which includes Master's degree + PhD. Although you already have a Master's degree, you can always apply for this one, if you think your application isn't strong enough for direct admission to the PhD. This is really your choice, you can always contact them to ask further questions.
You can find further information here otherwise.