Just found a fantastic site. Go to www.csa-railroads.com. The railroad that we are discussing was The Alabama and Mississippi Rivers Railroad. The author of the site provides links to maps and sources. It appears that at first they unloaded the cars and put everthing upon a steamboat at Demopolis. They then proceeded to McDowell's Bluff where they reconnected off loaded and reloaded just as you surmised. I haven't found anything about the ferry yet.

Bob