What do you mean? Are you trying to prevent  others from hotlinking to one of your directories (folders) or the files therein? I think you're misusing the term "hotlinking" -- please explain what you're trying to do.

Howdy-On the Hotlink Protection page, when URLs are added to the "Enable Hotlink Protection" box, does that mean that only the URLs listed will be able to link to the sites?
I need to have some kind of hotlinking to allow my subdomain to link to files, but I would prefer not to allow anybody to link to my sites, so I'd like some kind of link protection.

OK, you're misusing the term "hotlinking". Hotlinking is when someone steals your files (usually images) and bandwidth  by displaying your images on their site, but you're paying for the hosting and bandwidth. "Hotlinking protection" is putting code in .htaccess to prevent this, by explicitly listing which domains are allowed to use certain filetypes. Obviously, you want your own site(s) to be able to display your images, and you may want selected other sites to display them (e.g., your avatar on Lunarpages). cPanel has a feature to add hotlinking protection to your .htaccess file. By default it protects image files (.jpg, .gif, etc.), but you are free to protect other file types. I'm sure you could set up the RewriteRule to protect all files in one directory if you wanted to. And of course, you could have multiple Hotlink Protection sections to protect different kinds of things, each with its own list of permitted (whitelisted) sites.

Can you list your primary domain and subdomains and add-on domains, and what you have in your .htaccess file now? If you don't want to show this in public, feel free to PM the information to me. I'll let you know if I see any problems in .htaccess.