For this packages it's even easier since you actually don't need to install anything. Just drop the contents of the directory you checked out into the root of your project, and add the name of the directory to your INSTALLED_APPS settings.
So if you cloned out mezzanine-html5boilerplate just copy the directory out into your project like this:
(Notice that I changed the dash to an underscore, probably a name like "mytheme" might work better, but I don't want to complicate it)
myprojectroot/
/mezzanine_html5boilerplate/
/templates
/templatetags
/etc...
Then in settings.py change your INSTALLED_APPS so it looks like so:
.....<other_apps_snipped>
"mezzanine.generic",
"mezzanine.blog",
"mezzanine.forms",
"mezzanine.pages",
"mezzanine_html5boilerplate",
Then while you are working on modifying the theme, you will want to add:
THEME="mezzanine_html5boilerplate"
Which allow mezzanine to use the theme without installing it.
Why does this work? Or "why did I need to do this?"
Django "apps" can reside either in your site-packages directory or in your project itself. When you add that application to your INSTALLED_APPS, in a typical installation this will do a couple things (and more, not applicable)
If there is a directory called "templates" in that directory it will include it in the template_search path,
If there is a "templatetags" directory it will include those as well.
Hope that helps.
--Brent