Lee's a bit of an enigma in terms of tactics, having died without writing a memoir that let us get inside his head. However, there is still a lot of evidence out there we can use to piece together his mindset.

Napoleon of course defined military thinking in the 19th century, as probably the most successful general of all time. French was the language of war, and was a required language at West Point, as many of the instructional texts, such as Thiroux's Instruction théorique et pratique d'Artillerie were in French. Education there primarily focused on producing good junior engineering officers, rather than military strategists. There, the situation is a little fuzzier; it's quite probable that West Point cadets would have to read Jomini, probably Napoleon's greatest academic disciple, and if there was any military history on the curriculum, you know who would take center stage. In terms of Lee specifically, we know he attended extra classes while superintendent of the Academy, specifically those of D.H. Mahan, who was the head of the Academy's Napoleon Club. Unfortunately, due to the destruction of records by fire, it's impossible to ascertain his activities regarding the club. Fifteen of the 48 books he borrowed from the library concerned 'military biography, history, and the science of war.' Seven of these books concerned Napoleon. Furthermore, while we aren't necessarily sure Jomini was required West Point material, we do know that Lee both checked it out from the West Point library and owned a copy of his own, along with several military works (primarily in French), though sadly he didn't leave behind any notes or marginalia.

I believe there's clear evidence of Napoleonic influence in Lee's tactics in 1863. To me, Chancellorsville looks like a textbook case of Napoleonic use of interior lines and the Central Position; faced with essentially two armies, each larger than his own, Lee used a division and a few detached brigades to mask the enemy's East wing, while deploying most of his force against the West wing, defeating them individually, as Napoleon did at Jena-Auerstädt.

Pickett's Charge to me recalls more Austerlitz than Wagram, though I'm sure you're better acquainted with the latter battle than I am. Having attacked the flanks of the Union position on the high ground the previous day, the situation mirrored a protracted Austerlitz, where Napoleon drew the Allies' reserves to the flanks before launching his crushing attack on the high ground in the weakened center. There were problems with this approach though; I don't think there were any fences between Soult and Pratzen heights, and Napoleon's artillery ammunition actually worked. Lee's artillery did not have enough ammunition to support the attack while it was underway, JEB Stuart's cavalry failed to really contribute through the whole campaign, and on the whole, the Army of Northern Virginia was not the Grande Armee.

While Napoleon's men and Marshals were veterans of a decade of constant warfare, ACW armies were largely amateur, lacking the institutional experience for real combined arms decisive battle in the Napoleonic model. They lacked much in the way of dedicated skirmishers, heavy cavalry, horse artillery, shock infantry, and even more importantly, the skill and steel to use what they did have. Infantry usually failed to press in with the bayonet when the moment came; even in Pickett's charge, most of the men stopped short of the Union lines to shoot it out, and got shredded. To someone steeped in Napoleon's campaigns, the move was theoretically sound, but theory is not something you take to the battlefield.