When setting up a long document in inDesign, there are a few best principles to follow that will make your experience much smoother and enjoyable.
A) Use master templates. This is crucial, create a master template for every page type that you will be using in your book. A classic standard is a blank template without page numbers for end pages, chapter titles, etc; and a page template with the "page number" special character being used (and also possibly the name of the document as is often the case with books). Many other additional templates can be added if you have a way of setting up specific areas in the book, but it sounds like those 2 will be sufficient for you.
B) Set up paragraph and character styles. Probably the most essential part of your entire project will be having master paragraph and character styles to apply to your text. Determine your base font size, base line height, etc. and set it as your master paragraph style. From there, create children paragraph styles for headings, block quotes, etc. that fit your needs specifically. Whenever you want to modify the paragraph style, it will be changed throughout the entire document, which saves incredible amounts of time. Character styles can be used to style individual words within paragraphs, like pull quotes, drop caps, and other such items.
C) Section appropriately. Each document produced will have different sectioning needs. Some can simply be paged from 1-xx while others benefit from chapters and/or sections. inDesign has features available for each of these pagination types, I would recommend determining what would be most suitable for your specific projects and then researching how to achieve that function in inDesign. Beyond that, it's tough to provide you with specific feedback. The most simple example is to start your page numbering at the 4th or 5th page (or whatever page the content truly begins). This can be achieved through the pages view in the dropdown menu, explained very well at this resource: inDesign Pagination
D) Explore inDesign's built-in features. inDesign is a very powerful program and before Creative Cloud, it was reserved mostly for those in the industry. It has tools that can automatically generate indexes, table of contents, and many other literary tools. I won't go into depth for those here, but I encourage you to check out the resources available here and online. These features are not mandatory, and your project can be achieved without them, but they can speed up the process a lot.
E) Render for Print. Understanding how to properly render a PDF for print is a whole other topic, and rightly so. Some pointers would be to export it using the High Quality Setting and make sure that you specify your bleed if you have any pictures that you'd like to crop to the edge of your document. If you use the most recent high quality Adobe preset, your settings should be at a good enough mix to print well at a printshop.
F) Render for Web. While inDesign does not have this feature built-in, there are oodles of plugins from different companies that allow you to convert documents quickly and easily into eBooks. Here are a couple examples:
Blurb eBook Plugin for inDesign
Kindle eBook Plugin for inDesign
Best of luck in your inDesign journey!
