For such a requirement excel and VBA offer ABS function which converts -ve to +ve, thereafter you can compare the two numbers.
For example column A has all +ve numbers
A
300
400
800
Column B has all -ve numbers
B
-300
-400
-800
In Column C.....Now lets compare them using ABS Function
=A1-ABS(B1)
.....the answer is 0 ...means no difference.