Use Extra CSS (Properties ->Conversion - Common Options) to do this to every paragraph during conversion. For example:
Code:
p {
text-indent: 2em;
margin-top: .5em;
margin-bottom: .5em;
}
Note that Common Options includes specific option for space between paragraphs and (paragraph) indent. So if they don't work the Extra CSS might not work either. If so, my guess is that you don't actually have paragraphs (<p>) in the input ebook, but rather something that looks like them.