A good place to start gathering information about the American Civil War
The Confederacy: A Guide to the Archives of the Government of the Confederate States of America REF CD 3047.B4 1986
The Union: A Guide to Federal Archives Relating to the Civil War REF CD 3047.M8 1986
Encyclopedia of the American Civil War - A Political, Social, and Military History (5 vol.) REF E 468.E53 2000
Historical Dictionary of the Civil War & Reconstruction REF E 468.R53 2004
Civil War Almanac REF E 468.F85 2007
Encyclopedia of the Confederacy (4 vol.) REF E 487.E55 1993
Smithsonian's Great Battles & Battlefields of the Civil War REF E 641.W48 1997
RefWorks -- an online research management, writing and collaboration tool -- is designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies.
Set up an account using your UAA/APU user ID and Password, and start organizing and sharing your research.
Overview of Post-War Reconstruction http://www.digitalhistory.uh.edu/era.cfm?eraid=8&smtid=1
About the Ken Burns Series, The Civil War http://www.pbs.org/kenburns/civil-war/
Regimental Histories in the Library of Congress http://www.loc.gov/rr/main/uscivilwar/
Confederate States of America Documents at Yale https://avalon.law.yale.edu/subject_menus/csapage.asp
American Civil War Virtual Library http://www.vlib.us/eras/civil_war.html