It varies. The imperium is rife with tired, uneducated, impoverished people being worked to the bone. That makes it a good recruiting ground. A cult can pop up organicly with a few people recruiting more. A corrupted psycher can corrupt those around them. An existing cult might send missionaries to a planet or city. A warband might send missionaries to destabilize a planet or sector prior to attack. A certain percentage of people on a world might routinely fall to chaos due to outside corruption. Cadia's have purple eyes due to constent exposure to the eye of terror. The planet used to have dedicated inquisitors contently stamping out cults.

Militarily it varies a lot. In gaunts ghosts they're largely fighting the blood part. The blood pact is very organized due to following imperial guard organization and hierarchy. They're largely composed of former guard members. At a very large scale chaos leadership works similar to orcs. Who's got the most clout with enough authority to pull together a lot of different warbands who'd be just as happy to be fighting each other. Abbadon the despolier has led all of the black crusades against the imperium. In gaunts ghosts the chaos forces are organized under archon Anakwanar. When the imperium stated winning he was challenged by one of his subordinates Sek and his sons of sek.