Site B is an alternative gamemode where you have unlimited funds. However, you cannot place any buildings apart from hatcheries, lures and feeders. You can still terraform also. In Site B there is no particular objective. You have the ability to create dinosaurs and, rather than keeping them on display, let them roam free in a more natural way. You can choose your 5 dig sites upon starting, and the dinos related to these sites automatically have 100% DNA genome, so they can live longer.
Site B refers to Isla Sorna, where INGEN raise their dinosaurs before being sent to Jurassic Park to be displayed. Isla Sorna is the main setting of Jurassic Park: The Lost World, and Jurassic Park 3, and the dinosaurs seen here and not in the first movie, such as the spinosaurus, have not yet been brought to Jurassic Park, due to the park's disastrous failure. Site B is John Hammond's idea of leaving the animals alone and watching them thrive.