So, maybe the first couple of chapters are the hardest to write.
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.