I have searched the web far and wide to find awesome pre-made templates for iBook Author, because it seemed to me that I could not modify the pre-made templates at all. However, I found a quick and easy 7 step process to creating completely custom templates for iBook Author and am offering this tutorial free to you, the indie author. Here goes. Step One - Open iBook Author. For this tutorial, I am choosing the "Once Upon a Time" template, but any old template will do. Click "Choose".
Step 2 - Select the little Layout button (shown here) and then select "Show Layouts". This will allow you to edit the layout.
Step 3 - Edit Fonts. I can now select any font I want on this template and change it to a default setting of my choosing. I am publishing "This Broken Earth" (my post-apocalyptic extravaganza) as an iBook, so I will want my fonts to have a look that suits that genre. I think 1942 Typewriter will suffice. I'll leave the main body text alone, but I could modify that as well if I want to.
Step 4 - Use the Inspector. I can use the built in "inspector" to modify anything I want about this template. I can change the font size, modify the color of the font, or do a plethora of other things to the template. Understand that you probably want to keep the gutter sizes and other details the same because Apple is a little picky about iBooks looking just right.
Step 5 - Cool stuff. I can even modify the background paper (even though I would probably lighten this image a bit before using it to make the text more readable) This gives the iBook a different feel. Here I am changing the background paper by selecting "fill" -> "image fill" then choosing this scraped and rusted metal public domain photoshop background.
Step 6 - Apply Changes. When I click "Apply Changes" the template for Chapter Text will be changed to fit what I have been designing up to now. If you don't like it, you can always go back and change it. As stated, I would probably lighten the background paper image a bit to make it more readable. This is only an example.
Step 7 - Change the others to match. You will have to scroll through the layout menu to find the other template pages such as "copyright" and "dedication" to make them look like your other pages or you can make them look however you desire. Now that you have made these changes, each of your iBook pages will look exactly as you want them to look. I have also written a detailed tutorial on how to use Scrivener to create an iBook for iTunes. You can find that here.