Switzerland is a Schengen-country. Thus, the 90-day-period is the same as in any other EU-/Schengen country.
I think that the 90-day period starts when you enter Switzerland.
On the other hand, if you keep your address in Germany, carry your notification of residence and confirmation of registration at the Citizens Office with you, you perhaps aren't affected at all - but I would ask your "Ausländeramt" (or perhaps just the "Einwohnermeldeamt") before.
But be reminded that neither a valid residence permit nor a work permit issued by another Schengen member state (here: Germany) gives the holder a right to work in Switzerland.