Not sure where/how to start:
 

So i'm wanting to do the area between the framerails and the body on the truck (do the hardest thing first), but don't really know where or how to start:

Let's look at a few pics:

http://i223.photobucket.com/albums/d...ps8d2ea2d5.jpg

http://i223.photobucket.com/albums/d...pscb49cd04.jpg

1) Should the fairing in the second picture sit flush with the bottom of the framerail or is it ok in this position?

Any other suggestions/questions?

Not sure what you are asking exactly, but it looks like you're thinking bellypan when you might consider side skirts and get more benefit:

http://fixonroad.com/blog/wp-content...ide-skirts.jpg

https://www.capinc.com/wp-content/up...ttachments.jpg

Nice images of the inner side skirts. For an underbody, I would advise including the lowest points of the vehicle. Also, I would advise starting with the front.

Starting with the rear (and allowing air to get in, aka, not stopping air from getting into it), will work like a bit of a parachute.