It's interesting, but not surprising, that a quick check of Hardee, CS and US Regs, and even Kautz doesn't list burials, funerals, or similar words among the provisions. Respect for the colors, proper saluting, etc. is the focus. I'd stick my neck 'way out and venture a guess that there was no standard, prescribed method of folding the colors applicable to The War period. Contrast the slow, deliberate and highly respectful manner in which the graveside ceremony is conducted today, respectful to the family, to the deceased, to the service. Then think of wartime conditions of the 1860s --bodies left to rot (or to the hogs); shallow, scooped-out burials; mass burials in trenches -- hardly a time for such things. Nor, as been pointed out, does the elaborate procedure of today sound like something thought out and mandated, as opposed to an evolved ceremony (probably evolving more in reflective, peacetime circumstances). Similarly the traditional firing over the grave (which I'd guess pre-dated flag folding concerns). Except as a rarety (such as the combat death of a commander) would the regimental -- let alone the National -- color or standard be given up for wrapping the corpse or covering the casket. This has been an interesting thread, and I hope it will be pursued in off-line research and study. What I sense as the short answer to the original question is that we don't know of any standing procedure (and rather doubt that there was one at the time), but that our sense is, that the key (as Tom and others have noted) is Respect for the symbol represented by the flag, observed with appropriate gravity and solemnity, as the occasion affords. (Remember the chaplain in Mauldin's WW 2 cartoon, with his ear cocked for "incoming," saying "...Amen -- hit the dirt," or something like that).