Working with primary sources is a good first step. There are many primary and secondary sources available including diary entries, images, and letters.
Here are some names of female spies that you can use in your research. Recognized female Confederate spies include Rose O’Neal Greenhow, Belle Boyd, Antonia Ford, Charlotte and Virginia Moon and Mary Surratt. Women wo acted as Union spies include Harriet Tubman, Pauline Cushman, Mary Elizabeth Bowser, Sarah Emma Edmonds and Elizabeth Van Lew.
Library of Congress Resources for Women in the Civil War, includes links to pictures, documents, and artifacts.
This link takes you to an undergraduate research journal entitled, "Never to be Forgotten: Woman Spies in the Civil War," by Hannah Wall. Her paper examines how Belle Boyd, Elizabeth Van Lew, Loreta Janeta Velazquez, and Sarah Emma Edmonds acted as spies during the Civil War.
This resource includes images and information about Civil War Spies.
Confederate Female Spies
Union Female Spies
This sounds like a really exciting senior thesis... I hope these resources will prove to be of some help!
Although the exact number isn’t known, it is believed that hundreds of women served as spies during the Civil War. According to the book “Women During the Civil War,” women spies often gathered information about the enemy’s plans, troop size, fortifications and supplies on scraps of paper or fabric and sewed them into their blouses and petticoats or rolled them into their hair. To smuggle goods such as morphine, ammunition or weapons, they often attached them to the frame of their hoop skirts or hid them in baskets, packages and even inside dolls.
The following URL address documents the woman spies and gives critical information about them.
The following URL address is from the Smithsonian and lists the top six spies that were women. Of course, the number one person given is Harriet Tubman! Nevertheless, it is a great resource!
This URL address gives a lot of information about Rose Greenhow who of course was a spy!
Finally, I am not sure what your schedule might allow; however, this URL address leads you to an event that will take place on August 29th-- might want to check it out!
Maxwell Battery presents the "Sisterhood of Spies" featuring stories of espionage, bravery, and romance. Learn about codes and ciphers and the women who used them. Follow the story of smuggling medicines across enemy lines and try come decoding yourself.