Hi. I've written a few books, self-published a few more and edit a magazine.
If you haven't got a publisher but want to get someone else to publish it, even as an e-book, best advice is to generate the text in word or some other word processor with as little formatting as possible.
Clearly indicate where photos/figures go in the text but don't put them in line
Keep all photos as large and good quality as possible, don't crop them. Keep as separate files. Number the files to match the references in the text
If you insist on writing on photos, also supply and unmarked version so the designer can do it properly with a decent font at the right size.
Captions as a separate list numbered to match the references.
Any figures the same as photos, but best treated as vector images and saved as high-resolution PDFs then the designer will see exactly what you see. They will have indesign that lets them edit pdfs.
Most publishers want figures and photos all numbered in one set, but not all.
If you have views about layout, create a fancy pdf version of your document as guide for the designer to ignore completely. It's highly unlikely the format and font they end up using will suit the proprotions of your example.
In other words, the basic rule is keep everything as simple as possible and let your editor and designer earn their money.
If you have a publisher, ignore all the above and follow the guidelines they will send you.
If you want to self publish, consider using Amazon and follow their online guides, however they probably won't let you embed multi media. If you want to do this, consider getting an advanced publishing program or even publishing it as an extension to your website.