Also ebay is a good place with numerous Joes grouped in lots for a few dollars. I generally don't care how good or bad of shape the figure is in, if I need a part, I'll use it, I don't care anything about value. If your just starting out customizing, you should start may working with some worthless, piece of crap figures like Star Wars. You can find the Badger paint at most hobby shops like Hobby Lobby. The flats dry fast and work great around the joints and doesn't chip, plus gives a better look of cloth.
Glossy paint looks best for parts like boots and belts or visors.
Keeping them like this will make it much easier to find the part your looking for. Then I dump everything out onto the floor in their own separate piles, trying not to get the parts too messed up. Then I just go through and decide what pieces work best together as far as function and looks. Once I get an idea, I just make a loose assembly of the figure to make sure the parts go together and make sure there are no damaged parts or constrictions. If you have arms with broken thumbs, don't throw them out, they can be repaired.