So if i understood, When i use a resistive voltage divider (5V example):
-> 0V become 2,5V (half)
-> -5V become 0V
-> +5v become 5V
Right?
Wrong.
-> 0V become 2,5V (half)
-> -2.5V become 0V
-> +2.5v become 5V
You have a 5V peak to peak wave, you center it on 2.5V.
Forget that some of the codes mean negative values, you don't need to know. In fact they will automatically be in ones complement form but you don't need to do anything with that knowledge.
So what i should do about the PWM port?
Absolutely nothing, just pass it the values from the A/D if you want to use PWM as your D/A. Otherwise pass the A/D values to the D/A you are using.
The values to send to the 'other' arduino are simply the A/D values from the input.