Artist Jaime Jones first did Magic art in Eventide and illustrated several Jund cards in Shards of Alara.
The first step of the creation of a card's art is its art description. The art description tells the artist what the card will do, what its flavor is, and what the mood of the illustration should be. Here were the instructions given to Jaime for Progenitus:
Color: Creature of all five colors
Location: Naya (see below)
Action: This card represents Progenitus, the legendary five-headed hydra-god that is the soul of the world. Show this hydra busting out of the ground in the Naya jungle, a being of incredible might and invincibility. It has stylish traceries of Magic's five colors (white, blue, black, red, green) etched into its skin.
Focus: The hydra god
Mood: enormous, Apocalyptic, uber-powerful
Progenitus is a key creature in Naya's mythology, and it was important that it seem, well, mythic.
Here's the initial sketch that Jaime submitted:
That clearly looked great. The heads needed a little more definition and the background needed to be jungled up slightly, but other than that, this was an ideal image for the legendary soul of the world. Jaime was given the go-ahead for the final version:
Here's the card in its final state, as you'll see in booster packs of Conflux.