I'm learning javascript, so this sort of issue doesn't really make sense to me, but I gather this is a specific issue with C and it has to do with how large integers are handled. Fair enough, but I'm actually quite curious how you should solve this kind of problem in a low level language and why.
You just write a function that returns -1, 0, or 1. It's not specific to C, it's in any language that has fixed-size types.
Another reason (a lame one) to return -1, 0, or 1 is that often the caller expects one of those return values for some reason (because the caller is dumb and your comparison function is replacing another one that behaved that way).
