Whether you're with a small press, or have independently published, getting your book in smaller bookstores is something you will likely have to take an active role in. If you have a small/indie bookstore in your neighborhood chances are this might be something you want to do. The best way to start is to establish a customer relationship with them beforehand. Visit the store often, talk to the clerks, the manager, learn their names, make it personal.
When you're ready to approach the store about carrying your book here some tips that will help.
#1. Have a short pitch/blurb in regards to what your book is about ready. It should be something you can say in less than thirty seconds, short and to the point. A one-sentence tagline is great for this kind of thing.
#2. Bring bookmarks and/or business cards with you to leave with the store so they can hand them out to their customers.
#3. Bring a copy of your book to give to the store's book buyer or manager (in small, independent bookstores they are often the same person).
#4. Let them know if you're available for author signings, readings, or appearances and what you're willing to do publicity-wise for such events (i.e., advertising in the newspaper, web, etc.).
Hint: It never hurts to buy a book as you're dropping off your bookmarks and the copy of your novel for the manager. Don't forget to follow up with the book buyer/manager a short while after you've given them your book. Drop in and see what they thought!