Quote from KyoShinda
After looking at the wiki for 5min I figured out it's common sense. Sorry if you don't see it that way. You only have to know a couple things and you're set.
Your post makes no sense. You looked it up (therefore probably required an explanation) so it's common sense? It's basically impossible to know these "couple things" unless they are explicitly presented to you, and they are not in the game.
And the reason the potions are confusing is because there's no way to intuit what the ingredients do, or even that alchemy exists without someone telling you beforehand. I guess you could say nether wort imbues things with magical properties and is therefore a base reagent, but then what about glow stone? What about ender pearls? What makes nether wort special? It is never explained. Then, you use other reagents with no intuitive meaning to produce the various spell effects. Why blaze powder for strength? An apparently flammable substance making you physically stronger? How is this supposed to make sense? Why not say, a bone? Bones contain calcium which is an essential element in skeletal muscle contraction. THAT would make sense. There's no way to know blaze powder could produce such an effect without a long trial period or meta-gaming.
This is why the OP is confused: the system has so little foundation in reality that it cannot be intuited.