A Civil War regiment was typically ten companies. In the very early days of the war each company could have its own flag with one of them being chosen as the regimental banner if a special flag had not been presented to the regiment itself. The phenomenon of company flag pretty well died out in early 1862 when the standardization of regimental battle flag patterns was ramping up.

During the war a regiment could have from one to five flags. Flags wore out, where shot up and sometimes captured and when that happened a new flag was needed. Once the Confederate supply system had ramped up the depots issued the flags through the chains of command.

This is the very short version to your question.

Greg Biggs