The Techno Union (I think that's what they're called) helped supply the Separatists with droids, and I believe the Separatists also made their own. They combined their forces (Remember the meeting with count Dooku on Geonosis. That's what they were talking about.)

Well, different droids had different Manufacturers. Battle droids, Super BDs, and droidekas were manufactured by the Trade Federation. Some spider droids were manufactured by the Union others were manufactured by another company (can't remember the name)