Unfortunately when you are working with a file that has been converted using Calibre it is more difficult to determine which class does what...it doesn't use descriptive class names, just numbers.
However the process is the same. Open a chapter and find a normal paragraph that you would like to have indented. Most of those paragraphs SHOULD have the same class. Right click on the <p class="..."> and "go to link or style" you can edit or add "text-indent:1.2em;" there.
However...the styling MAY be overridden by other classes depending on several factors. You would have to really study the Spec to determine the numerical priority it determines....*shudder*...
If the first attempt doesn't cause all your normal paragraphs to indent as you wish, then you can go to the top of your css file (just below all the .calibre styles and find the .p style. (this is really a quite ridiculous name for a class just to define the style of a paragraph: <p class="p">
) You can try adding your indent there.
If that still doesn't work, then add your own style to the CSS by defining all paragraphs to have an indent as default.
p {text-indent:1.2em} (notice there is no "." in front of the p)
This SHOULD not effect the other paragraphs that are not supposed to be indented, but YMMV. I can't really tell how the html calls the different classes without seeing the code.
The last thing to think of...or maybe the first thing...does your reading device (kindle) allow you to set the paragraph indent within it's properties?? I know Marvin does - tap the "aA" at the top of an open book and you can select the indent you desire by tapping on the two "Paragraph indent" buttons. That is the easiest place to fix it but it will only apply to that book on that device - it doesn't change the file itself.