|Honestly, would you want to have your world conquest defeated by a bunch of preening teenagers?|
Organizing all the elements required for a novel can be challenging. I struggled with it a lot writing Magnum Thrax and the Amusement Park of Doom.
I now use sticky notes and cue cards, a tool taken from screenwriting.
If I have multiple characters with arcs, I create a set of sticky notes for each, detailing the steps in their emotional journey.
I use cue cards for scenes. They're easy to move around. Key plot points are usually key character points, so there's a good deal of overlap. But using stickies as well allows flexibility as you build the character up (or down). If I just work with plot points, character development becomes secondary and I lose track of the arc I'd planned. It's much harder to keep track of everything than you'd think when looking in from the outside.
I the cards and stickies all out on a board broken up into three acts, with the middle act being twice as long as the beginning and the end ones. I then place down the stickies on, or beside the cue cards.
This helps give me an overview of the writing 'battlefield' if you will. I can coordinate the various character arcs and the plot, see it all at a glance, and move things around as need be. Sometimes you want to spread out your arc more, or condense it, or you'll realize you can align the arcs of characters in an interesting way. If you can find different colors for your stickies, so much the better. You know where each character has a major transformative moment.
Use different color pens to note positive or negative changes. Have fun. Do what works for you.
Of course, once I have my outline done and start on the first draft, I often find myself going off track. I'm not saying my process works, or that I follow it perfectly, just that it helps me organize things in the beginning. Lays down the race track. My bad driving is another problem altogether.
An effective character arc can be easier to plan than execute.
You can find lots about structure in books like Blake Snyder's Save the Cat. Hero with a Thousand Faces by Joseph Campbell and The Seven Basic Plots by Christopher Booker are also very good. They give a nice break down of plots frequently used in mythology, which also run in tandem with the character arc. In fact, plot elements are really just externalized representations of what's going on inside the main characters head.
Buffy the Vampire Slayer was great for that sort of thing. They'd use the poor, doomed monster-of-the-week to throw into sharp relief a flaw, or personal dilemma, of one of the main characters. Tempt their greedy side. Play on their idealism. When you start from that position, it gives the story a very strong emotional hook. Sometimes, it really IS all about them. Very solipsistic in a way: the villains attempt to take over the world and cast humanity into everlasting darkness only happens to help a main character learn a lesson about sharing.
Personally, if I was a villain, I'd be rather put out. Let's not sugarcoat this: it takes a lot of hard work, planning, dedication, and determination to take over the world. People are always trying to stop you. Let's not even get into the logistical difficulties, or what to do with it once conquered. To have such a grandiloquent effort reduced to minor lesson in the life a whiny adolescent would make it so not worth trying.
But then, we read mostly for the emotional connection.
Something to get better at.