The thing you have to remember is that different moves have different recovery times - so if someone whiffs a move with fast recovery, you either shouldn’t try to punish it, or use a really quick (not much start-up) move, like close jab, or whatever her fast normals are. Basically, that’s the general starting point - what’s a fast normal that I can start a combo with? Will I have time to do close HP xx Hayate? Or, if they whiff something that has huge recovery, like Ryu’s Ultra 1, what should you do with all the time you have? You don’t want to end up panicking and throwing, 'cause that’s a waste of a good opportunity.
It depends on the game, yes; in MvC3, assists and special moves that don’t connect give you no meter. Also, note that in games where you get meter for whiffed moves - they’ll give you more meter if they connect - blocked or hit. Some moves (normal moves in SF2, SF4) don’t gain meter unless you connect with them.
You go a little bit at a time - like when you’re looking at a guide and you think to yourself, “Wait, what does he mean by ‘Fierce’?” then you come back here, etc, and you figure it out. That’s a basic example, but for more complicated ideas like hitstop or frame advantage etc, you kind of take it in as you need it. You have to start learning from playing, most importantly.