You will want to consider posting this question on the Civil War Flags Message Board at http://history-sites.com/mb/cw/cwflags/

Greg Biggs, other vexillogist, and other flag related subject matter experts are infinitely familiar with what the regulations said vice what may have been practiced in reality vice the overall trends.

Respectfully,

Gerald D. Hodge, Jr.
M.A. Military History - Civil War Concentration
Research - Preservation
Historian: 39th Georgia Volunteer Infantry Regiment