I found a workaround for my problem:
I createt a new function which works between my App and Simulink.
In Simulinks Matlab Function Block I was able to call the function with the Matlab engine:
coder.extrinsic('FunctionName'); % On the top of the MATLAB Function
%Then you can call the function
FunctionName(...);
Using this I was able to use the same global variables in the called function as in the App Designer.
I hope this helps, if anyone has the same proplem as me.