Intake and output is not math, it's arithmetic. No matter what the liquid is, you add the number of cc that went in (Intake, I) and the number of cc that came out (Output, O). That's pretty much it.
If they want to know what the balance is, that means that you lok at the difference between intake and output.
If there was more intake than output, the patient is in positive fluid balance (positive here is not necessarily a good thing-- it means a positive number, greater than zero). Do the subtraction.
If output was greater than intake, that's a negative fluid balance (negative is sometimes a very good thing indeed, if someone was fluid-overloaded in the first place and you want him to pee out more than he takes in). Do the subtraction.
Does this make it clearer for you?