How can I change a section's title color by editing the template in iBooks Author?
The layouts easily editable when using the graphical interface of iBooks Author. 

Close any documents you may have open to avoid confusion and then open a new document from the template chooser. Start with a template you like and …


View menu -> Show Layouts
make your changes to fonts, colors, layout, etc… on each type of page, working your way down the list.
File menu -> Save as Template…


At that point, save it in the default location and when you start a new document, you can choose your custom layout for starting a new book.