Unless you own your own building or are making significant interior renovations, all you may need to implement are 36-inch wide aisles and a checkout counter that can be accessed from a wheelchair. If you are catering to parents and/or small children, you'll find the wide aisles necessary for strollers as well. And if you plan to accept trade-ins, the lower counter height is convenient when someone staggers in with a heavy box of books.
Next, call your local fire department and find out their regulations for retail shops. My fire department requires a main 42-inch wide aisle running from the front of the store to the back and a fire extinguisher near the front door. Some fire departments also regulate how close merchandise can be to the ceiling, so make sure to ask about this.
If you will be adding any interior walls (perhaps to partition out a back room), get the contractor in and have him tape out where the wall will go, how wide, etc. Then get out your tape measure and some graph paper and make a to-scale chart of your selling space.
If you will not have a back room or other storage space, your selling space will also have to include somewhere to put overstock, display storage, supplies, etc. Some stores handle this by making their wall shelves as tall as possible and putting overstock on the highest shelves. Others just shelve in all their overstock. Or, perhaps like in department stores, you can store supplies inside or under some of your display fixtures.
You may wish to start by mapping out your cash wrap, as that will be the hub of your shop. Typically a cash wrap is placed near the front of the store so that you have line of sight with the front door and can monitor customers coming in and out. If possible, I prefer the cash wrap to be anchored to a wall, rather than a kiosk in the middle of the store, otherwise you'll have people trying to ask you questions from all directions at the same time. Make sure to leave enough space in front of the cash wrap for customers to line up comfortably.
My cash wrap has one checkout station. The front counter is six feet long, but I wish I had made it eight. My cash wrap is L-shaped, with another four-foot section of wooden counter hooking the Formica to the wall. The front of the cash wrap includes some display shelving. The backside of the cash wrap also has shelving for supplies: bags, receipt tape, etc. Behind the counter, against the wall, is a low bookcase that holds special orders, reference books, strict-on-sale merchandise, etc.
The more tasks you are planning to accomplish at your front counter, the larger it will need to be. Also, the larger your store, the more checkout stations you will need. At 1600 square feet, I can get by with one, but when it gets really busy I wish I had a second station. If you will not have a back room and will be processing mail orders at your cash wrap, then you will also need a shipping station with room for boxes, bubble wrap, etc.
I process incoming inventory at my cash wrap. Since the counter is high, I have a small table beside my chair that I place the boxes I am working out of so that they will be at a comfortable height. Since we accept trade-ins from customers, I have to have a place to store the books I've accepted and those that customers have left to be donated (we donate to our local FOL group, which comes once a week to pick them up). I put the merchandise I've just purchased behind the cash wrap on the floor between our special order bookcase and the main wall case. Donations are placed at one end of the cash wrap. Make sure to consider needs such as this when designing your cash wrap area so that boxes of books do not impede your traffic flow.
Next, jot down the various sections you'd like to have in your shop and try to assign a percentage of your shelving to each one. For instance, perhaps you want 25% of your shelf space dedicated to Classics and Literary Fiction, 20% to Children's and Young Adult, 30% to Nonfiction, and 25% to gift items. It doesn't matter what you decide, so long as you get it down on paper as a guideline. Start with large categories like the above and then try to fine-tune any breakouts that you may be envisioning. For instance, Classics and Literary Fiction could include these different subsections: Poetry, Drama, Regional, Multicultural, Award Winners, etc.
Before penciling in any fixtures, think about how you want your shop to feel: Do you want an open, airy feeling or a cozy shop with cul-de-sacs and towering aisles so that customers feel sheltered and private? If security is a concern, then I suggest low open-ended aisles that can be easily seen over. I'm short (5'1") and usually the only employee on the selling floor