Actually it's easier than you think. Go into the ACP>Thread Prefixes>Thread Prefix Manager now either make a new prefix or edit an old one.
Once you reach the screen where you set the ID, title, etc, you should see a link below the two title's. Note, you'll need to save the prefix first and to this screen if you're creating a new one. Click on the link beneath Title (Rich Text). It'll popup a tab/page called Phrase Manager. Here you can use Html code to stylize your prefix.
For instance, if you wanted a green colored [Accepted] prefix, you would use the html code:
HTML Code:
<span style="color: green;">[Accepted]</span>
Note that all code must go in the text box just above the save and reset buttons.
Also note you'll have to add the prefix title manually like I did in the code. It replaces the generic title with the colored version.
If you know html and the style property you can make some pretty amazing prefixes. I used backgrounds on the ones I made. Theoretically, I haven't tried it myself, you could even use images as a prefix.
Hope this helped ^^