The Htaccess/WebDAV section of the panel does exactly two things:
[*] Lets you set up simple password protection for directories ("htaccess"). The login for these directories is kind of inflexible and unfriendly, but at least it's simple to set up. I'd only recommend it for very simple tasks, like if you need just want to have a site you're still working only accessible to people who you've given the password to.
[*] Lets you set up WebDAV directories. If you don't know what these are, you don't need them. (It's a system for uploading and sharing files which is used by some mobile applications.)
If you're getting along without any of these features so far, that's fine. You can ignore them all, and you'll be happier for it.