Hi!
Thank you neil for your advice!
I got rid off the "no previous declaration" errors! 
But.... 
Now i am facing 58 errors like: undefined reference to 'GetTickCount' in wiring.c, undefined ref. to 'PIO_GetOutputDataStatus' in digital_wiring.c...and so on.
I only include Arduino.h like in the temporary compiled cpp from the arduino sdk.
Please help me out! This is so demotivating! I really don't know what i am doing wrong!
This was so easy with Uno...i did it many times without these strange probs....i am looking forward to loading the code up from atmel-studio... =(
Can't somebody post a compiling example-atmel-solution?
That would be great!