This is the topic that can generate an endless amount of debate and input. Having been a reenactor and student of Civil War uniforms and equipment, and a painter of historical minis, I have taken sort of the middle road with this one.
I had some really good discussions and brainstorms with TMP member Avidgamer, a super fellow, extraordinarily knowledgeable and we really are on the same wavelength.
We talked at length about what "average" or "generic" confederates should look like.
I want to say that I really admire your historical awareness of your figures in terms of the time period of the war, the theater, etc. That goes a long way in determining the color choices you make for uniforms.
For confederate infantry, you can go with two schools of thought, or a combination of both.
As Frederick said, a generic style of browns, greys for uniforms you really can't go wrong. Throw in some captured sky-blue federal trousers on some of them and you have a pretty good average.
One thing that can really make a miniature confederate army come to life is if you throw in some sections of troops that reflect some of the exceptions.
What I mean is, while you are doing the majority of your confederates in a mix of brown or grey jackets and trousers, also put aside a few stands of infantry and purposely paint them in ALL matching gray jackets and trousers AND caps. This would reflect the times during the war where there was a consistent uniform issue to a large body of men, as did happen in the Army of Northern Virginia at times.
An example would be after Gettysburg, just before Longstreet's corps was sent to the western theatre to take part in the battle of Chickamauga, his entire corps was issued with new suits of bluish gray jackets and trousers, but the problem was they were on the much bluer side of gray, and looked a lot like weathered Union uniforms. Their uniforms did cause some confusion at Chickamauga because of the bluish color.
So in that instance, you have 1863 mid-war, and an entire confederate corps wearing more or less a consistent uniform, or at least it remained consistent until things began to wear out of course.
The other thing you can do in the middle of the generic ranks is throw in the occasional gray cap with the blue infantry band, which was issued on occasion.
For equipment you have some really clear and distinct options. Since captured federal gear was so common and so prevalent during the war, you can freely paint haversacks, canteens, and blankets in Union issue colors. same goes for knapsacks even. Union issue haversacks would be black, canteens would be covered in brown or tan cloth, blankets would be brown or brownish gray. Confederates also widely captured Union cartridge boxes and belts, which would all be black.
Another widely captured federal issue item was the federal issue rubber or gum blanket, which would be a glossy black.
You can paint some of the blanket rolls in glossy black to represent the issue rubber blanket being rolled on the outside of the bedroll.
In the mix of all the capture federal gear, you can also paint a fair percentage with actual confederate issue gear. The confederacy produced cartridge boxes in both black and brown leather (russet). They produced haversacks in the black waterproofed versions, but the most common they produced were plain white haversacks. Their issue canteens were often of the metal drum variety, so those could be painted a metallic silver.
As far as straps go, canteen straps could be white or brown to represent cotton drill, webbing, or leather.
Finally, for shoes, again the confederacy produced leather shoes in both brown and black leather, so a mixture of those is perfect. Confederates of course also used thousands of pairs of captured federal issue shoes which were of black leather.
Hope this helps!