I gave a talk at the genealogy club I belong to. My topic included online sites for searching for a Civil War ancestor.
You’ll want to go first to the Soldiers and Sailors Database at the National Park Service. It includes a database of Civil War prisoner information for sites like Andersonville and others. I recommend printing out any information that you find online. Sometimes sites or databases disappear.
To order Civil War pension records, try this site.
As you know much genealogy information is only available online through subscription sites. For military records, I hear many recommendations for fold3. I haven’t tried it yet, but probably need to quit stalling and give it a whirl.