I've seen this question (in one form or another) has been asked a few times here, here, here, here, here, here, and here, however, either the questions haven't been answered at all or deal mainly with Kutuzov.
I know this is a big question (and book) and I don't expect one person to be able to answer all of it, but I would love to know what the general opinion is of Tolstoy by historians regarding his history in War and Peace. My only real knowledge of Napoleon's invasion of Russia comes from this novel and I worry that Tolstoy's arguments many be far too one-sided in favor of the Russians.
I don't have a great answer for you, but I do have a good source you can consult. A friend of mine knows the author and says it is essentially an attempt to figure out just how historically accurate Tolstoy's depictions of the war are.
Rick McPeak, Tolstoy On War:Narrative Art and Historical Truth in “War and Peace.” Ithaca, NY: Cornell University Press, 2012
I do not know why any historian would use War and Peace as a guide or source for that particular time period. Tolstoy was an author and a moral essayist, not a historian. His own comments on the work included a the statement that it was not, in his own opinion, a historical chronicle. To use common, modern terms, the book could be called historical fiction. Tolstoy did use quite a few primary sources to help establish the framework of the novel and to ensure the history was correct, but these elements are more functional than anything else. By that, Tolstoy used those primary sources to make sure he had dates, uniforms and the like correct as well as the overall flavor and setting of the French invasion. A good portion of the book contains his own moralizing and philosophical musings, so I would argue that this colors the entire book and perhaps clouds any historical facts. Having certain themes and ideas he wanted to illustrate or muse through in the book would cause him to focus on certain events, or fictionalize others to make his point, so again, it should not be read as a history text. Tolstoy was interested in portraying the Russian experience from a Russian point of view, so again, it is going to be Russian biased. I would not use the book as a primary source of the time period anymore than someone should use "North and South" mini-series for US Civil War history. The book is a product of a 1860's Russian intellectual looking back, through the views of an 1860 Russian intellectual, on the history of Russia. Entertaining, relatively historically accurate on the macro level, not so much on the micro, the book should not be seen as a primary historical source.