Hal:

See Lonnie R. Speer's "Portals to Hell: Military Prisons in the Civil War" (Stackpole Books, 1997).

I found "Hope Slater's Jail" for blacks described in Baltimore, Maryland. It was used circa 1861-1863 and temporarily housed Confederate POWs from Gettysburg en route to other POW camps.

Hugh Simmons
Fort Delaware Society