All right, buckle up, this will probably be a little long. 🙂
First, there are some basics you need to have in general. A quality book goes without saying, but it will need to be in one of the major wholesale networks and will need to be returnable (one exception on returnable that I'll get to later). You need to have a good "sell sheet" ready to go, and I recommend having a media kit on your website. Those two things you want to have whether you're reaching out to bookstores or not. I don't consider myself a pro on that, but you can go to my website and click media kit and see what I did (the media kit includes a copy of the sell sheet). Google it and you'll see roughly a million different views on the media kit, so just do what works for you.
So, on to bookstores. Step one is just getting together a list of bookstores in the first place. I started in my state, then expanded to the rest of my region, then ultimately to the whole U.S. Unless your name is Max Lucado or Joyce Meyer you can forget the big chains - we're looking for independent stores. There are a few lists out there, like the Logos-affiliated stores, but I didn't get very far with those lists (with the exception that I'm in the Logos store in Nashville). What I did, which was very time consuming, was do a google maps search for "Christian Bookstores in <state>" and just go through the list. Some you can skip right away, like the big chains. There are also a bunch associated with christianbook.com that you can skip. Catholic stores almost always exclusively do Catholic books, which there's nothing wrong with, but if you don't have a Catholic book you can skip them. Stores that end with ABC are Adventist Book Centers, which are fine, but like most Catholic stores they only do Adventist materials. Same with Christian Science reading rooms. And finally church bookstores tend to sell only denominational materials or if it's a megachurch only books from their staff, so I pretty much skipped all the church bookstores. I'm telling you all these to skip so you can save a lot of time up front and have a more manageable list.
All right, I told you to search for bookstores, and you may well have a better way to do it than I did, but what information do you actually want? What you ultimately want is the name and email address of the book buyer, i.e. the person who decides what to stock. With most independent stores that is just the owner, but the bigger ones have another staff member to do it. With some you get lucky and that information is on their website or Facebook page. For the best results as far as getting the right person, you call the store during business hours and ask whoever answers the phones. About half the time, with small stores, the person who answers the phone is the book buyer and you can actually break the ice on the phone. Sometimes it's the opposite and the person on the phone is clueless and you spend time explaining what you mean by book buyer and eventually they give you an email address. Making the phones calls is also time consuming, and for those of us with day jobs kind of tough because the bookstore hours are often the same as your work hours.
Now you've got a list of bookstores and the names and email addresses of the person who makes stocking decisions for them. This is when you need the sell sheet. You send an email to the book buyer (and if you spoke with them on the phone make a reference to that), you say you have a book you would like for them to consider stocking at their bookstore, give the two-sentence version of your elevator pitch, make sure they know it is available and returnable through a wholesaler, and attach the sell sheet. Marketing types recommend you also include some incentive for them, like including them in an upcoming ad campaign. I did this (the ad just being a boosted post on Facebook, which is cheap), and while some of them expressed appreciation after they saw me give their store a plug, I'm not convinced it made the difference in anyone giving me a chance. A book and pitch they are interested in is worth far more. The other thing you do in the email is offer to send them a PDF copy or paperback to review - after all you're really just asking them to review it for consideration at this point. If you don't want to spend a few dollars on mailing a paperback, just offer the PDF, but I had quite a few who wanted a paperback only (it lets them check the quality of the book).
I'd say 80% of the stores will never respond to you. After your first emails go out, wait two weeks and send a follow-up to the ones you haven't heard from. The ones that want a review copy obviously send one as quickly as possibly. After you send it, give them a few weeks and check back to see if they have had a chance to review it yet. Don't pester them but check back at appropriate intervals until you're sure you aren't getting anywhere.
I mentioned one exception to returnable, and that is that a few stores want to do consignment. I have three stores doing consignment basis, which basically means it's your money sitting on the shelf in the form of inventory instead of theirs (for some small stores they can't afford much inventory). It's up to you whether you want the hassle and expense of doing any on consignment, but I decided it was worth it. I also have one store that just purchases straight from me at a steep discount.
One other thing that is worth mentioning is that there are plenty of general market bookstores that happen to be owned by Christians. So I'm in a couple of those. I didn't spend a lot of time on general bookstores, I just reached out to a few in my general area that have "local author" sections. I've done some book signings at those as well.
Bonus points: I donated two books to my local library system. The library people will tell you it actually helps sales, but I think that is more true if you have multiple books or if you have a series and just donate the first one or two. Mine finally made it into the system about three months ago and the copies I donated have been checked out pretty much non-stop.
Double-bonus: My friend wrote a book (Sir Barton and the Making of the Triple Crown, for the horse racing fans), and was shocked to discover it on the shelf at our local Barnes&Noble. She honestly didn't know how it happened, until she found out her friend went to the store to order a copy. I haven't tried this with my book yet, but the theory is that if someone orders it at the store it signals demand and they'll stock it at that store. Feel free to try that and let me know if it works.
Whew, I think that covered it, but please let me know if you have questions or if some part of that didn't make sense to you.