How does a computer deal with subtraction of 2 values that are in two's complement?
If you are working in 2's complement, that means that ALL the numbers are in 2's complement form. That is, a positive number will begin with a '0' and a negative number will begin with a '1'

So if A and B are two such numbers and you want to do (A - B), then you 2's complement B and add to A.