Personally, I think it is experience. I think the key is to understand what the fish is supposed to look like. For most species there are pics of wild fish in their natural habitat. I use those pics as a guide. If my fish are fatter than that then I am feeding too much, bellies more hollowed than that then the need more food. Eventually you figure it out.
How old they are also matters. I am much more willing to overfeed juvenile fish a little while I would rather have full size adults on the healthy but hungry side.
I have found that there are no universal feeding amounts. I have some fish that all the food is gone in less than a minute and others that need 30 minutes to get it all. It just depends on the fish and their feeding behavior.
For me, the bigger challenge is finding the right balance of food that ensure that everyone gets fed. It is too easy to get only half the tank fed sometimes. Feed flake or floating pellets and the upper level fish can get it all before the bottom dwellers. Feed sinking pellets and some top level feeders won't get to eat unless you get the timing just right.
