The quote from the movie is that the planet that Krall/Edison crash-landed on contained a "drone workforce", presumably some sort of (biological?) robots which would explain the sheer quantity of men and ships at his disposal.
Edison: The indigenous race abandoned this planet long ago. They left behind
sophisticated mining equipment and a drone workforce
That being said, we see several different species without their helmets on. I think we can assume that since he's not stuck on the planet that he was also recruiting from other nearby races that hate the Federation.
As to who was flying the ships, they appear to be controlled by the drones, following the orders of the small number of actual biological pilots.
Spock: Captain, the flight patterns of bees are determined by individual
decisions. Krall's swarm formations are too complex not to rely on
some sort of unified cyberpathic coordination.
This has now been confirmed in an interview with director Justin Lin and screenwriter Simon Pegg
"That's what the swarm is – sophisticated mining equipment. All those soldiers were just worker drones. Krall turned them into an army, and
turned the swarm into a weapon. There's all this great backstory to be
explored in the novelisation!”"
Star Trek Beyond: 12 things we learnt from Justin Lin and Simon Pegg