I think I faced a similar dilemma with one of my novels which contains a flash back in time in the middle of telling the story. To prevent confusion for the reader, I actually decided to start the novel with a prologue which set the stage for the alternate History ... since the theme of the novel is a 'what if' for the reader.
Perhaps you could begin your novel by relating the historical events of Chancellorsville, sort of like a journalist relating it to newspaper readers of that era, as a prologue to open the novel and set up the notion of an alternate History. Then, start your first chapter with the alternate History immediately confronting the reader.
Thank you!
What kind of novels do you write?