My question is, I want to upload my book to Amazon and iBooks. I can create the correct layouts for these platforms (iPad H/V and Kindle H/V) using Alternate Layouts. Right now I've completed the iPad version. I should be able to upload this to iBooks. If I want to do a version for Kindle, do I have to duplicate the document and format a separate layout for Kindle, or can I add the Kindle layout to the existing document? I have that option, but what about uploading to online stores? Would a single document with 4 layouts - iPad H/V & Kindle H/V work for both, or should I do 2 separate documents?
I think you're confusing the features required to creating digital publications and need to do some more study.
If you want to upload a book to iBooks, you need to learn to create an EPUB file. You can't do that with the Alternate Layouts feature. When an EPUB file is created (by choosing File > Export > EPUB) most of the appearance of the InDesign file disappears. The appearance is determined by the CSS and HTML that is exported in the EPUB file. There are a series of things you need to learn to do to make the text ready for EPUB; learning how to format graphics; setting up paragraph, character and objects styles and learning how to map them to HTML; learning how to create a table of contents in the right format; learning the correct settings to use in the EPUB export dialog; etc.
It may even require editing the CSS in an editor to achieve your required appearance.
Amazon Kindle uses a different format referred to as MOBI or sometimes Kindle format. It has many similarities to EPUB, but requires some kind of conversion. Many EPUB publishers use a utility from Amazon called Kindle Previewer to convert EPUB files to Kindle format. Again, this has absolutely nothing to do with using the Alternate Layouts feature.
I'd suggest you do some more research. Two good places to start: (1) Books from Elizabeth Castro available at her website:
And videos created by Anne-Marie Concepcion on the Lynda.com website for InDesign CS5 and 5.5 (the one for CS6 should be along before too long).