You cannot have different prices for the same store but for websites, if you do not use a custom extension which allows this functionality in case you want it.
For the websites you can enable this the following way under
System > Configuration > Catalog > Catalog > Price
Then you can't show different currencies in admin, only at the frontend.
So what you should do is to create two websites, set different currencies for both. And then in Admin enter both prices in base currency using conversion rate (e.g. 100€ for Website A and 50 CHF for Website B).
Then the conversion will work in the frontend as you described.