I'd like to see the story of Bobby writing to the Kansas School Board as the main story, maybe in live action, and the explanatory bits done as memories or imaginings with CG.
So, for example, we have Bobby leaving university and pondering what to do with his life.
He has a day dream about the FSM creating the mountains, trees and midgets.
He reads in the paper about the KSB introducing ID into science classes.
An explanatory bit about how he 'met' the FSM.
Maybe a bit where he discusses Pastafarianism with freinds, and their reactions. I suggest they are eating pasta which bobby ends up using for the purposes of illustration. Maybe a short Heaven sequence after this.
The KSBs response to Bobby's letter.
Bobby sets up the churuch of the FSM.
The End (until we make some money to make the sequel?)
The end credits could be shorts of Pastafarians in full regalia saying hi from whereever, or whatever witty things tend to be said in that kind of outro.
In other words, the true general story, but with imaginative segments regarding the creation, heaven, hell, whatever other parts of the adventures of the FSM you care to add.
May the noodly goodness flow upon you.
And then the FSM extended His noodly appendage, tasted the Holy Sauce of Life, and declared It good.