iBook 'Master' contents page?

Which template did you start with?

Try a couple others, such as 'Basic' or 'Comtemporary' to see if a different style suits your needs better.

Screenshots can't hurt...

Have you tried to use the layout for preface, change it to your needs and use it to put your main content with links to other parts of the book? Make that page the first page in your book. You'll have to create a series of bookmarks and point each link to the appropriate bookmark.

I had to do something like that recently for a client who insisted having a more traditional TOC in addition to the built-in TOC you get with iBooks.

I see what you're trying to do. Unfortunately, in order to create your own TOC (that's in effect what you're trying to do) can only be done by adding a page at the start of the book. Since you can't add a page, you have to use the layout for chapter or section. The advantage of using something like the preface layout to do that is that your chapter numbers will not change. "Born Yesterday" will remain chapter 1. See the way I did it in a recent iBook I created for a client (Note that I could have put the page "how to use this book" as the intro media, thus eliminating it from the TOC)

Here's a quick mock up using the same concept but only with a content list page at the begining. I used the preface layout to create the content list:

I'm pretty sure you were hoping for something different, but I think this is the only way you can do this. Let's see if others chime in.

You can only create a bookmark by selecting text that is not placeholder or chapter title, section title, etc. The best way is to click anywhere in your text on the page you want to bookmark and then the "+" will appear. The bookmark is to a page not a part of the page (unlike anchors in HTML), so it really doesn't matter where on the page you create your bookmark.

I know you can't add a bookmark to the chapter text fields. I think your problem is that in the layout itself, only objects tagged as body can be bookmarked. For example, in the IBA basic landscape layout (floral structure), you will notice that you can't bookmark text in the box in the first page of a chapter (below the chapter title. That box is tagged as "introduction". The other chapter pages are tagged as "body", so when you put your own text (replacing placeholder text) you will be able to add bookmarks in these pages.

One way around that would be to remove the intro text box from the first chapter page (in the layout view). You then drag the blue arrow which you see from the top of the second page box to the first page, click and drag to create the new box. This links the 2 boxes and since they have body as a tag, you can now add bookmarks. Or, if you are early in your project, maybe you can select a template that has already objects that allow you do what you want.

I hope this helps.