As with most everything else Confederate, a small book could be written about CS footwear. I suggest you start out on this web page:
http://missouribootandshoe.tripod.com/index.htm

This will give you the basics. Good place to purchase them also but not the only place.

Both North and South experienced spot shortage of shoes. Most of the time it was on campaign and the supply wagon had not visited in a while. The South was more prone to shoe shortage at other times but at times they had footwear aplenty. Again, a broad subject.