A valid question! Authors can find it tricky working with independent bookstores, for lots of reasons. Here are some general tips:
1. Is your book published through one of the Big 5 (Hachette, Simon & Schuster, Penguin Random House, Houghton Mifflin Harcourt, Macmillan) or a well-distributed press like W.W. Norton, Workman, or similar? If yes, you can reach out to a store requesting that they stock your book. You’ll want to demonstrate that you know what they sell (check their staff picks online, go visit the store and see what’s on the displays) and mention what makes your book a good fit.
2. Is your book independently published, and/or only available through wholesalers like Baker & Taylor or Ingram? If yes, you can also reach out to a store requesting that they stock your book, but the approach is going to be a little different. Many bookstores won’t take chances on books they have to order through wholesalers because they can’t easily return them if they don’t sell. If you’re willing, offer to sell it on consignment (wherein you only get paid if the books sell). And do all the above – make sure you know what the store does well with and why they should consider your book.
3. Regarding follow-up, if you don’t hear back: personally, we believe one follow-up, a week or so after initial contact, is just fine.
If they stock it, well done! If not, c'est la vie. Limited shelf space is the number one reason indies don’t order books; they’ve got to try and keep in what sells well. Some stores (like our Jersey City location!) have a special consignment program for local authors. Others may not take consignment at all. It just depends. Good luck, and congrats on publishing your book!