Hi fjtorres,
It's not really an edit of the epub. It's more a case of setting some personal preferences at the time of creation. Admittedly, it's not as good as being able to change them at will during reading. (This method isn't really necessary anymore on a Sony PRS505 since the excellent hack development of PRSPlus)
Re: margins. I think the usual way to control margins during a Calibre conversion would be on the [Convert] - [Page Setup] page where you specify top, bottom, left, right explicitly.
Calibre's Extra CSS facility is very powerful though. You can add pretty much any CSS you like. I often use it to control the space between paragraphs by adding
p, div, li {margin-top:0.25em; margin-bottom:0.25em;}
I know this is something else you can do on-the-fly in fbreader
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