Exploit the setting guide
Stonetop comes with a lot of established setting, but it leaves a lot of blanks for you and your players to fill in during play. The setting is intended to serve as a springboard for your creativity. It helps set a tone and gives you all a common starting point. It provides details to riff on. It hints at answers but doesn't always give them. Use the established setting to portray a rich and mysterious world.
Use the setting guide to inspire, but don't feel beholden to it. If your players give you something that contradicts the established setting, don't negate their input just because the book says so. The book isn't the authority, it's a resource for you to exploit.
With that said: be thoughtful about what you change or discard. It's safer to change specific details than to change broad themes. If the Fox says that Brennan used to run a gang in Marshedge and killed his way to power (as opposed to the setting guide's story about how he was a bandit who the council hired as their marshal), then no big deal. But if you and the Seeker decide that the Makers were gnome-sized tinkers instead of inscrutable titans, then you'll need to rethink all sorts of setting details (the size of the roads, the scale of the Ruined Tower, the themes associated with each type of Maker, and so forth).