Maryland's state flag was not official until 1906 when the present flag was made to reconcile the state in regards to the families who fought for both sides in the war. The black and yellow stripes are from the Calvert family (the proprietors of the colony). Those who were faithful to the north favored these colors during the war. The red and white Bottony (correct spelling)cross are of Crossland family, maternal family of Lord Baltimore. Those families who were pro Southern wore red and white as susession colors. Beast Butler outlawed the civilian population in Baltimore to wear the colors red and white, but somehow, the colors flurished anyway. The Bottony Cross was also worn by the Maryland troops in the Confederate army as an ID, just like the Palmento Tree for the South Carolinians and the Star for the Texans.
Many veterans of the war (from both sides) belonged to the Maryland Militia after the war, and it was the members of the 5th MD Regiment who first displayed what is now the state flag.
During the War, the state did not have an offical flag, the one most widely used during that time period was one with the state coat of arms (still used today)on a dark blue filed. The Marylanders that fought for the South also wore belt buckles with the state seal on them. It is documented that the 1st MD Cav, CSA had a flag that was the Red and White bars of the First CSA Flag and replaced the stars in the blue canton with the state seal. I have no evidence that the state seal was used on any drums or such by the CSA troops.