If you are separated or divorced you are no longer eligible for simplified naturalisation. You can go through normal naturalization process once you hit the 10 years mark. How long are you in Switzerland already?
What I understood from your post is that you've been married for a bit more than 5 years and going through simplified naturalization.
If you separate, you will automatically no longer be eligible; it is best you stop the process yourself right now if you go through the separation.
Even after naturalizing through this process, they can reverse your citizenship if you divorce within a few years from the date you obtain it. And, they definitely will check.
in the moment i am looking for an apartment. we are not jet officialy seperated. we are still living together but in seperate rooms. i have found an Apartemnt and will move in it in December.
what do i have to expect, when i move from the apartement where i live with my wife?
When you find an apartment, you will have to officially change your address. At that time, I would ask whether there are any other administrative tasks you have to perform, as, if your permit is tied to your wife's, they might require you to get an independent one (which should be no problem in case you've lived here for >3 years married, IIRC). Just don't apply for citizenship on the basis of your marriage, as that marriage is in trouble.
After 10 years in Switzerland and on a C you can apply for citizenship using the regular process.