Well, there's two distinct and very different schools of thought at work here. Let me see if I can capture the essence of both.

1) The Well-Supplied Confederate

This theory, proposed by many modern researchers, has established that Confederate troops were well supplied once the supply system got going. Those letters about starving, ragged soldiers stem from spot times of short supply, such as at the end of drawn out campaigns, etc. Those letters are also held up by the "Lost Cause Faction", a group of folks from the South that insist that all Confederates were without shoes, and most fought in long underwear with string pouches holding their meager supplies and crumbs of food. Often, pictures of Confederate dead at Petersburg are exhibited for proof of this theory, as all of the pictures of the non-surviving Confederate dead show them well clothed. (Please ignore the bare feet shown in these pictures.) The proponents of this theory steer you to file cabinet after file cabinet of official Confederate Government documents (see, they still smell like smoke from the Richmond fire) showing the expenditure of millions of dollars on uniform purchases and importations. Ream after ream of paper from the Quartermaster Department (and the six surviving examples) shows undeniable proof that in 1864 Richmond you couldn't swing a dead cat without hitting a Type II Depot jacket, or whatever the nomenclature is. The fact that almost all surviving examples of Confederate uniforms show some wear and tear on them, well, they were worn during a war, you know, and (here's the dismissive generalization) more than likely worn after the war as regular clothes, since you see the military buttons removed from so many of them. The proponents of this theory are referred to as "Revisionist Wackos" by the other side.

2) The Starving, Barefoot Confederate

This theory, purported by many traditional researchers and old-time historians, selectively uses hundreds of reminisces from veterans, those reminisces mostly from Veterans speeches of the 1880s and 1890s, to insist that all Confederates were without shoes, and most fought in long underwear with string pouches holding their meager supplies and crumbs of food. Often, pictures of Confederate dead at Petersburg are exhibited for proof of this theory, as all of the pictures of the non-surviving Confederate dead show them without shoes. Pictures of gaunt Confederates are trumpeted as indelible proof, notwithstanding the fact that most of the people that had their picture taken in the 1860s were gaunt by our standards. Voluminous Confederate Government records indicating tens of thousands of uniform purchases and distributions are dismissed as proof that the government could supply the uniforms, because the distribution system was so bad that the soldiers never really got these uniforms and they all burned up when Richmond and Atlanta burned down anyway. This logic indicates that the Government needlessly spend millions of dollars on uniforms that stayed in warehouses, while other items like rifles and ammunition were magically distributed to the troops. Unless of course you agree that all Confederate troops supplied themselves by taking what they needed from dead Yankees. This indicates that evidently Yankees also fought in long underwear with string pouches. The fact that almost all surviving examples of Confederate uniforms show some wear and tear on them, well, they were such treasured possessions and historic mementos that they were immediately put into the cedar chest upon the weary veteran's return from Appomattox, and never saw the light of day again, so they existed exactly as they did on April 9, 1865. This generalization assumes that: (a) All Confederates surrendered at Appomattox and (b) everyone had a suit of clothes waiting for them when they returned home. The proponents of this theory are referred to as "Lost Cause Wackos" by the other side.

The Henry Clay Compromise - Sometimes they were ragged and starving, sometimes they were well supplied. It just depended on where they were stationed and what time period you are discussing.