Let's say we have n1 and n2. I guess what you are trying to do is:
n1 = 41;
n2 = ~n1; (compliment)
41 => 0010 1001, then the compliment of this is n2=1101 0110
Now, since the most significant bit is 1, the resulting number is negative. In order to find this number you do:
1. 1's compliment of n2: 0010 1001
2. add 1: 0010 1010
3. this is 42, but since it is supposed to be negative, n2 = -42
Hopefully, it makes sense