Which Install document are you reading? The one included within the archive says,
You should never overwrite any files within your includes or the cache_builders/custom directories unless the version upgrade instructions specifically say to do so.
and further down, it says,
You will also need to copy over /styles/common.css and /styles/admin.css from the archive directory to your corresponding forum styles location. Be careful not to overwrite your /styles/wrappers.php.
It then has a link which points to here:
https://www.ubbcentral.com/forums/directme.php?to=threads_upgradeThat url should answer most of your questions. If anything else should come up, please feel free to discuss it also in that thread, so others can benefit from the given help.
Cheers