There is no px program... PX stands for pixels and what he meant was that you should define your margins in px instead of %.
Not to be disrespectful, but try to look at some CSS and (X)HTML files and try to read something about them. It is not hard, but some basic knowledge about them is required when you start to tinker with ePub files.
For editing I personally use notepad++. You could use
tweak_epub to select and update the files in a ePub.
Enjoy your journey!