As far as I know there is now to subtract strings, that said I am no expert. What you can do however is extract the number from the string and then perform you calculation.
Do you really need strings? Even if I had to implement such a long number algebra, I would use arrays of some numerical type.
Anyway, the simplest way to do it, is think of how you do additions and subtractions on a paper: start from the least significant digit, do it, then do carry, etc.. If you use strings, you need to convert each digit to a number (either by a simple subtraction, and knowing the ASCII codes, or using library routines).
Either there is a function in the standard library, or you write it yourself. But strings are always very slow. If speed is an issue, use arrays of bytes (or chars) instead.