How does the equivalent exchange of alchemy work?
Alchemy has three stages: Understanding, Break down, Rebuild.

Different alchemists have different specializations because of the Understanding part, learning chemistry in general isn't easy, and digging into a specific subject (For instance, the study of the atmosphere and oxygen in Roy Mustang's case), is even harder, hence specialization.

Matter of "equal value" means of equal "type" (Mineral to mineral, organism to organism, you can't turn stone into a flower), and of equal Mass.

This works well in accordance to the physical laws of matter and energy conservation. You cannot make matter disappear, nor you can make it appear out of nothing. You can't input more matter to be on the safe side, that matter won't be used for the alchemic transmutation (at best), or result in a rebound (at worse).