As John mentioned, the main manuals are about the same in what they prescribe for composition and actions of the color-guard, but as Bernard pointed out, what units actually did could vary. Judging from battle reports, the color-guard in the field was not always or maybe even very much of the time composed of nine men. A review of reports in the Official Records from 1862 shows color-corporals or other men from the color-guard often taking up the flags when the color-sergeant fell, but when you start looking at reports from 1863 and 1864, the soldiers who took the colors after the color-bearer fell often seem to have been from some different company and not necessarily part of the color-guard. A number of reports record officers taking the colors after the color-bearer fell (4th Arkansas and 6th Kentucky at Murfreesboro, and 53rd Virginia at Gettysburg are examples). In at least one case, a Confederate regiment seems to have not had a standing color-guard, and "drafted" men into the color-guard for battles (this was the 5th Texas at Gettysburg; the citation is in William Fletcher's Rebel Private Front and Rear, though Fletcher apparently had an axe to grind about carrying the colors and his description may not be exactly what happened!). The 18th U.S. Infantry at Jonesboro reported that its color-guard consisted of two sergeants and two corporals (OR Series I Vol 38 Pt 1 p 586).
Having served as color-sergeant in large battalions in the 125ths and later, I can see dispensing with the color-guard's third rank, but the rear rank of the color-guard is essential because they keep the spacing correct in the front rank of the battalion during advances, and make sure that the center of the battalion stays behind the color-bearer and keeps the six pace distance. But I would imagine that units in the war did have those five men marching around the colors; perhaps they just weren't always "officialy" designated as the color-guards.
Curt, it's just as well that the 105th OVI kept that Indiana flag cased at Perryville, because it would just have been shot full of holes by Maney's men anyway! (that's one of my favorite Perryville stories, too)
4th Kentucky Infantry, Cotton States Battalion
Honoring Ensign Robert H. Lindsay, 4th Ky. Vol. Inf.
KIA Jonesboro, GA August 31, 1864
Roll of Honor for Murfreesboro and Chickamauga
Member, The Company of Military Historians