[PF] Making a Campaign - The Grand Scheme

[Sheogoroth]

So I'm making this campaign...

I want to spread it out over 5 story Arcs and it embed it very strongly within the PF universe and plot.

Essentially, there are 5 foils to the party- a former group of Pathfinder society heroes who were seduced by forces of the Cthulu-esque dieties of the Dark Tapestry. The Arch of Aroden(a big old stone land bridge) is actually a giant inactive portal that the Nega-Heroes are trying to use to summon an Elder Evil to devour the Starstone and bring a thousand years of darkness etc.

Each story arc is going to revolve around the PCs either dealing with, trying to thwart, or attempting to hop one step ahead of one of these Nega-Heroes, which one of them being the Big-bad of each arc.
I also wanted a unique tone and genre for each arc, slowly ramping up the heat from sleepy Murder-Mystery Noir an apocalyptic race against time for the finale.

I'm a relatively inexperienced DM, but I'm really excited. So a few questions:
1. I've gone through several versions of the plot in an attempt at simplification, but the plot still has the potential to get convoluted- I really don't want my players to get confused/disinterested. Is there a good way to mitigate this?
2. One of the anti-heroes is actually some kind of dragon. I've been looking for a dragon that was relatively powerful, but lacked the alignment restrictions of Chromatic/Metallic dragons- something less iconic. The idea is to have a sort of "Aladdin in the Cave of Wonders" arc with a dragon's hoard at the end. Any kind of dragons really stand out for this situation?
3. What's the best way to deal with PC housing in a long campaign with lots of travel? Should I just leave them to their own devices?
4. The campaign has 5 villains, at which point should I show the party who these guys are? That is to say, they won't actually show up unless totally necessary, so generally there's only going to be one per arc. So how do I keep an engaging Hero-Villain dynamic going on?
Am I overthinking this?

Any other tips you can give a green DM would be greatly appreciated!

[NightbringerGGZ]

1) Without more details I can't give anything more than general advice. I'd use each of the 5 villains as an opportunity to play with various modes of combat. Maybe one is a pirate and you have to track down his ship and engage in naval combat. Maybe another has control of a dungeon you have to explore. Try taking the players through a variety of regions, cherry picking some of the cooler stuff from various APs.

2) Why would an actual dragon have been a society member? What about using a Dragon Disciple instead?

3) Let the players decide what they want to do. It's more fun for everybody that way and encourages role playing.

4) I'd set up the first couple as just bad guys and have local quests lead you towards taking them out. Leave hints that something bigger is in the works and reveal it around Act 3. Act 4 could be about prepping to take down the final guy(s) and the final Act should be about large epic fights.

[Bigbeefie]

I like the dragon disciple surprise. Build up the fear of fighting a dragon and then suprise them.

If you go dragon pick a black dragon. Red, blue, and white are all played out and major resistances. Keep his color secert and I am willing to bet they won't have acid resist running and will take a beating from poisons.

[Vanitas]

Pathfinder has primal dragons, which are not chromatic or metallic. You could use that.