Well...it really depends on how detailed you want to get. A great deal of the comics running out there are established in real and current cities like New York, New York or San Francisco, California. When that is the case you just use the real city and it's landmarks. Sometimes you need to alter names of places that may be a copyright issue, but you can keep your favorite bookstore as long as you don't use their logos.
You should know that Gotham City is really New York City during its darker days with the major landmarks given a more gothic look with different names. Metropolis is really New York City as well at it's most sun-shiny with everything given a more modern look.
My best advice is to use the map of a city in existence that fits the shape you are looking for and just change the names of the businesses you want to use. Drive or walk around the town you live in and take note of what lies in relation to everything else. Questions to ask yourself are:
1. Where will my characters live? Rural? Urban? Suburbs?
2. Where will they hang out? Home? Mall? Arcade? Pool? Coffee House?
3. Is everything within walking distance? Do they have to drive? Car or scooter/bike?
4. Where will they work? Mall? Office building? Warehouse?
Answer these questions and create these locations first. Then you can begin to flesh out the buildings around them and use them in transition shots.