Hi. I find two different settings for 50p filming in my pmw-200 settings. It is in the camera menu "system" where i set 50mbps/422/720/50p
And then there is S&Q Motion where i can set on/off and set a frame rate. How do i set these settings?

Unless you want to over- or undercrank, leave S&Q motion OFF. The basic frame rate setting is done in the 'system' menu, as you have correctly suggested.

S&Q stands for "Slow and Quick", or in film terms "Overcrank and Undercrank" and takes more or fewer frames than "normal" and applies them to the clip to give you slow motion or fast motion using entire frames and not frame blending or interpolation.