There is the Cemetery for Hebrew Confederate Soldiers in Richmond, Virginia. This is detailed, with names from an 1866 plaque, over at the International Jewish Graveyard Rabbit.
There's a section on interesting Union and Confederate articles, such as the Confederate Passover Seder, which is a letter written from South Carolina by Isaac J. Levy of the 46th Virginia Infantry to his sister, describing how he and his brother celebrated a Civil War Passover:
April 24th, 1864
No doubt you were much surprised on receiving a letter from me addressed to our dear parents dated on the 21st inst which was the first day of פסח [Pesach]. [note from LMB: Orthodox Jews are prohibited from writing on Sabbath or a festival] We were all under the impression in camp that the first day of the festival was the 22nd and if my memory serves me right I think that Ma wrote me that Pesach was on the 22nd inst. Zeke [Isaac's brother Capt. Ezekiel J. Levy of the 46th VA] was somewhat astonished on arriving in Charleston on Wednesday afternoon, to learn that that was the first סדר [Seder] night. He purchased מצות [Matzot] sufficient to last us for the week. The cost is somewhat less than in Richmond, being but two dollars per pound. [For point of reference, Matzah in New York City was then 6 cents a pound. LMB] We are observing the festival in a truly Orthodox style. On the first day we had a fine vegetable soup. It was made of a bunch of vegetables which Zeke brought from Charleston containing new onions, parsley, carrots turnips and a young cauliflower also a pound and a half of fresh [kosher] beef, the latter article sells for four dollars per pound in Charleston. Zeke E. did not bring us any meat from home. He brought some of his own, smoked meat, which he is sharing with us, he says that he supposes that Pa forgot to deliver it to him....
Read more at the link above. Levy was 21 when he was killed at Petersburg on August 21, 1864; he's buried in the Shockoe Hill cemetery. His letter is preserved in the American Jewish Archives, in Cincinnati, Ohio.
There's also an interesting section on Samuel G. Alschuler, known as "Abraham Lincoln's Jewish Photographer," who was born in Bavaria in 1826 and was a photographer in Urbana, Illinois when Lincoln visited to have a portrait made. The photographer even loaned him a velvet-collared jacket for the occasion.
And for the female view of this history - she married into the famous Sephardic Seixas family of New York City - here's a diary section written by Eleanor Cohen Seixas, Southern Patriot, dated February 28, 1865-September 10, 1865.
This illustrates the importance of writing a journal. Your diary might become very important to your descendants.
There is much material on the site, and another section is a full article index of the Jewish newspapers, The Occident and American Jewish Advocate 1843-1853. Articles include information about many topics and Jewish communities.
Look at the extensive list of links at the site, which may prove helpful to researchers.