I haven't used Cpanel in a long time. I'm sure there's a way to create directories using it.
Your dilemma is more with the "one click install". I imagine there is a way to have it install into a sub-directory as well, but maybe not.
But as long as your host gives you FTP you can install it wherever you want. It wouldn't be "one click" but IMHO it isn't all that more difficult.