How to get domain.com/~user and not ip/~user

Your second desired method (/~username by hostname instead of IP) was disabled in a past version so that bandwidth usage was counted properly. You can undo the changes if you want, however bandwidth usage will not be counted if clients use that address to access their website.
http://www.directadmin.com/features.php?id=392

Probably the easiest way to do what you want for the subdomains is create the user accounts using that subdomain $username.$hostname.com as the domain. This has been discussed before.
 
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