When you create categories there are some check boxes at the bottom to pick which ranks can view any boards inside that category. (like an Admin only section is a good idea to have the category hidden from non admins)
This will show you how to edit the view permissions if you created your ranks AFTER you created categories.
(click the page&magnifier to edit that category)
After which you can create your boards in pretty much the same fashion.
(click the page&magnifier to edit that board)
This will let you decide even further who can view, reply, start new topics, start polls or who can moderate each board.
The only other permissions to be able to give out are admin permissions.
Each panel has a "rank view" setting on it to select the ranks that can see it. and it is pretty much the same for the rest of your site.