In Lee's hometown of Monroeville, Alabama, the Ol' Curiosities & Book Shoppe has seen tremendous support for the book.
"Sales have been great we've done 8,500 to 9,000 copies," said owner Spencer Madrie. "A lot of those were pre-ordered, but a lot more are on the way."
Read More A new book, but an old conspiracy theory
At The Strand, a large, independent bookstore in Manhattan, 15 copies of "Watchman" were sold in two hours Tuesday morning, marketing manager Whitney Hu said.
"We still see palpable excitement and curiosity among customers this morning, despite the NYT review," she told CNBC via email. "Most readers don't seem to mind discovering a more nuanced Atticus Finch, instead of a simplified heroic figure from the first book."
Sales of "Watchman" also reignited interest in "Mockingbird," with copies of the 1960 novel being scooped up by customers, she said.
In Oxford, Mississippi, hometown of William Faulkner, paperback copies of "Mockingbird" have already tripled the usual yearly average at Square Books, said owner Richard Howorth.
Read More Nationwide and Across the Ocean, a First Glimpse of 'Watchman'
"Almost as soon as this was announced, people began to reread or read for the first time 'To Kill a Mockingbird,'" he said. "The whole publication so far, what stands out to me is that it's given everyone an opportunity to re-evaluate 'To Kill a Mockingbird.'"
Howorth said that people have excitedly attended events centered on the two books at his store, and that customers were waiting outside Tuesday morning at 7:30 to get their hands on a copy of "Watchman."
People are very curious about the notion of Atticus as a racist, Howorth said.
"Some people say 'I can't believe this, I'm not going to read this,'" Howorth said. "I tend to think those are people who wouldn't read it anyways. Other people say, 'Get over it, I'm interested, I'm reading it.'"
Amicucci said readers will decide for themselves about Atticus.
Amazon senior editor Chris Schluep said the response in customer reviews for Kindle and print have been overwhelmingly positive.
Schluep said the ability to compare "Mockingbird" and "Watchman" is a reason to buy the book.
"Authors are supposed to write what they know, and I'm sure [Lee] knew many more men like "Watchman" Atticus than "Mockingbird Atticus," he said.
Sarah Crain, past president of the Virginia Association of Teachers of English, said "Mockingbird" is still a staple in high school libraries, and "Watchman" presents a new learning opportunity, but it shouldn't be just a history lesson.
"We should look at letting students explore this option and countless other options for how you maintain your humanity in the face of overwhelming prejudice," she said. "I would rather see this as a larger array of texts that students could choose from as opposed to seeing another teacher manual that had comprehension questions for every chapter."