[yann]

1) You have to put in publich HTML directory in order to access it via "your_domain.com"

"your_domain.com" points to public_html/ contents...

I don't recommend to create the webdisk as the "root" like you describe it unless you're only going to access it via WebDAV. From everything I've read, accessing directories via both WebDAV + STP/FTP can create problems... Although I have no idea how cPanel handles it... But I would a webdav specific folder in my public_html if I were you (via webdisk cPanel utility)

EDIT: I should mention that if you create you webdis say like: public_html/omnifocus/" when you enter the url in OF prefs, you shouldn't include omnifocus folder like "http://your_domain.com/omnifocus" but just "http://your_domain.com:2077" the server knows which folder it is from the user account you sign in from

2) the "SSL (recommended)" checkbox" only changes the way the "bookmark" you're downloading will connect to WebDAV folder.

https://your_domain.com:2078 or
http://your_domain.com:2077

ps: weird that you don't need to include @xxx.xxx for user name - that's pretty standard for webdav I think