A long-time link at the Soldiers and Sailor's site bears mentioning. If you haven't seen it already, take a moment to view the flags at this online exhibit: Symbols of Battle: Civil War Flags in NPS Collections. It features photos of some of the banners in the collections of nine different National Park Service sites (Appomattox, Ford's Theater, Ft. Pulaski, Ft. Sumter, Gettysburg, Kennesaw, Manassas, Richmond, Stone's River).
The flag above is at Kennesaw, and interestingly, it is the flip side of a Confederate First National flag. The motto of these Cherokee Dragoons is "Either With it or Upon it," not a phrase in common use today, and not one that lends itself to easy explication.
The United States Treasury Guard's flag at bottom is at Ford's Theater. The caption reads: "Dramatically associated with the close of the war, this flag decorated the front of the Presidential box at Ford Theater, in Washington, D.C. on the night of April 14th, 1865. Booth, President Abraham Lincoln's assassin, caught his spur and tore this flag as he jumped from the Presidential Box to the stage below."