Funny you should bring up assembler, because this is for an assembly language class (the prof is going over a little about how a computer actually does the math) :p
Ok, so I believe I have figured out the answer. Because this was defined as a system that uses "unsigned (ie positive)" numbers only and ignores all negatives, it does not take the possibility of a negative answer into account (as it cannot have a negative at all). Using only 1 two's complement, I can get the correct answer to any subtraction that will result in a positive answer:
just to be easy: 8-3 = 5 (I did a few more on paper, but yeah, that would make this a big post)
8: 0000 1000
3: 0000 0011
------------
Doing the two's comp only once gets:
0000 1000
1111 1101
-----------
0000 0101 = 5
So if you dont ever think you will have a negative number, this is all that is needed. Because my problem was for "unsigned numbers" only, I did not have to check if the problem would result in a negative answer (which is impossible), and could stop at that step. As you pointed out, the next step involved putting a negative sign in front of the answer, which I cannot do as it will be rejected (and positive 88 would be wrong anyways). Well, thats all I can think of to explain it, I will see if I can ask in class, but that will be a while.
Once again, thanks for your help and the quick responses Octarine!