Then you give those special cases a class name:
Code:
CSS
li.space {margin-top:2em}
HTML
<li class="space">Part I</li>
<li>One</li>
<li>Two</li>
<li>Three</li>
<li class="space">Part II</li>
<li>Four</li>
<li>Five</li>
<li>Six</li>
<li class="space">Part III</li>
<li>Seven</li>
<li>Eight</li>
<li>Nine</li>
edit:
You can even go crazy and give them 'spiffy'

formatting just by changing the CSS like this:
Code:
li {text-indent:2em}
li.space {margin-top:2em; text-indent:0; font-weight:bold;
color:blue; text-decoration:underline; font-size:1.5em}
OK...I went a little crazy on the formatting....but I just wanted to show that you can format your book any way you want to very easily by setting up the proper CSS. It will really help to spend a couple hours reading those tutorials and picking up some basics of CSS.
Cheers!