Consider using HTML as an intermediate target format in all cases. Since the majority of e-book formats revolve around some variant of HTML, it might be a good idea to standardize on HTML as the format to export to first from whatever program you used to edit the document. This minimizes the amount of processing that has to be done by the e-book converter itself. What's more, if you need to perform any manual editing on the file to get it to process correctly, HTML is a convenient format to do that: You have direct access to the source code via nothing more than a plain-text editor.
Test the results on multiple devices. Get your hands on as many reading devices as possible -- or, failing that, get in touch with people who have a number of different reading devices and get feedback from them. The desktop Kindle application, for instance, has quirks that the actual device does not (e.g., how each handles non-Western characters), so it helps to know when problems like this are relevant.
Be prepared to repeat as necessary. You will almost certainly have to make multiple passes across an e-book to make sure everything translated correctly. Odds are it won't -- at least not the first time -- and you'll have to go back and tweak many different things by hand. In a way, this is another argument for using HTML as an intermediate format, because many of the tweaks that might need to be carried out could be partly automated. Keep notes of what breaks each time so you don't have to repeat your mistakes.
The creation of any e-book starts with a source document: a manuscript that you have written or that someone else has provided to you. Right there, the problems begin, since even a "clean" document can pose conversion difficulties. Your goal is to ensure that the document's formatting will be preserved intact.
Odds are most documents used as a source for an e-book will have to go through at least two conversions: first, into a format that the conversion software can use, and then into the actual e-book format -- or formats. Sometimes this can be cut down to one stage, but it's best for the time being to assume you'll need two steps to do the job completely.
Here's a rundown of the most likely formats you'll start with:
I already mentioned this in the previous section, but it bears repeating: If you're looking for a standard, HTML is more or less it. For one, it's ubiquitous; almost every text-processing program can generate or read HTML. It also supports many features e-books will use: hyperlinks, font control, section headings, images and so on.
Sign up for CIO Asia eNewsletters.