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The problem with your question is that there really is no general answer. Much of it depends upon the specific reader. For example, consider page size. In eReader, you don't really have control; the software resizes the pages for the device, so the same file viewed on a Palm TX (320x480 screen) will have a different page size than on a TE2 (320x320). And Plucker, for example, doesn't use pages. The entire file is one long "page", much like a web page.
Margins can be set by the user on eReader Pro, but are fixed for eReader Standard and Plucker. The user can select his own fonts for eReader Pro and Plucker, but not the standard eReader.
And I'm sure that there are many more variations with other readers. (Those are the only ones I'm familiar with.)
As far as tools to create the books go, the best I can do to help would be a guide I wrote for creating eReader books, based on text or Word files. You'll find it at:
http://www.memoware.com/?screen=doc_detail&doc_id=13409&p=contributor_id^! 19684~!
Hope that helps!
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