The first order of business is usually to grab a table, especially if your neighborhood coffee shop or bookstore is often crowded. If there's an empty seat next to someone, just ask if it's empty. Bring a sweater or jacket with you so you can hang it over the chair that you claim while you go get your coffee.
Don't leave your laptop bag, laptop, purse, or other important belonging on the table or chair to hold your place. Maybe it's the environment, but people tend to let their guard down at a cafe. Don't.
If you do need to get up from the table and don't feel like lugging your laptop to the restroom with you, secure your laptop to the table with a cable like the Kensington MicroSaver Cable Lock (a wise investment also for traveling).