Guidons were carried by most units north and south. Some were elaborate some were nothing more than little red or blue flags. Also US units did carry their national colors, but would have also carried either a blue regimental banner or a state flag. You can go to the NY State Archives website and view some of their guidons. There are also a few CS ones out there, notably at the Museum of the Confederacy, but if you read the battalion drill manuals you will see that Guidons were needed for the drills, etc.

Lee