Originally Posted by mr ploppy
Epub is basically html in a zip file, so design it in an html editor. You need to design it like a 1990s website though, so that it will reflow to fit any device and work with any base font/size the reader has set. If you try to force a rigid structure like a magazine layout it won't work for everyone and will just annoy people.
If you have a Kindle, look at how the scifi and mystery magazines do it for their ebook editions. The free sample should give you enough of an idea of how to approach it.
This. You either need to reset expectations or you need to use a format that allows for such precise control over layout (like PDF, ugh). As an aside, that's basically what Kindle magazines are doing -- PDF wrapped in an azw container. They're not Mobi files (Mobi is much closer to EPUB than it is to PDF).
The only thing I'd change about your description is that you shouldn't
design like a 1990s web page (tables everywhere!! !! !! uu!!), but instead design like you should
be doing for the web today*, with fluid layouts that accommodate flexible display sizes and use CSS for styling. EPUB doesn't support everything that a modern browser would, but in general it can do pretty much everything you need in order to create a nice-looking layout.
To play in the web and ebook spaces you need to get rid of old "paper mentalities". You no longer have pixel-perfect control over every single element in your layout as you would on a piece of paper. Your reader might have a larger or smaller font than you wanted, or might be reading on a 320x480 screen instead of a 1024x768 screen, or (on the web) may be using user scripts and styles and/or ad blockers and proxies that filter, change, rearrange, redefine, and otherwise mold your content into how they
want to read it. If that's not something you're ready for, stick to paper.
* Unfortunately very few web sites are actually designed correctly. It's all too common to see fixed-layout sites with a narrow ~600px (or less!) content frame with tons of wasted white space on larger screens. Even MobileRead is not immune to this (it uses a fixed-layout design, though it's at least a generous 920px of content where many sites will dedicate as little as 300px for the main content panel). Most sites also define font sizes and margins in px, making it impossible to change font sizes for accessibility without resorting to full-page zoom (one of the worst inventions of modern web browsers, IMHO, a crutch made necessary because nobody uses scalable units like em or % anymore). Thankfully tools like Stylish for Firefox and Chrome and Greasemonkey-style user scripting allow users to take back control of the web. It's just sad that nobody cares about good web design anymore.