It is very simply!
1) Install the Plugin (like all other plugins) & Copy the CSS Files into a subdirectory of your style
2) Open the "browse_template.html" File
2a) Add the two lines into your HEAD Section
Code:
<link rel="stylesheet" href='templates/YOURTEMPLATE_NAME/styles/hoverbox.css' type="text/css" media="screen, projection" />
<!--[if IE]>
<link rel="stylesheet" href='templates/YOURTEMPLATE_NAME/styles/ie_fixes.css' type="text/css" media="screen, projection" />
<![endif]-->
Replace "YOURTEMPLATE_NAME" with the real name of your template
2b) Replace the "<THUMBNAILS>"-Tag with:
3) Save your files and your done!
If you have questions to a specific part please let me know.