Hello,
One of the main reasons for having multiple IPs per User account was to allow multiple SSL domains under one User account.
The only thing you need to make sure is that they're "owned".
Also, you should only have 1 domain on the owned IP (mainly for "additional IPs") because DA doesn't order the VH's with the additional IPs, like it does with the default domain.
DA will always ensure the default domain is first. This is so that, when using SSL, it's VH is first, and it's SSL certificates are used. (multiple domains can be on an owned IP, but only the first VH's SSL certificates are used).
http://help.directadmin.com/item.php?id=89
With additional IPs, you can still have multiple domains, but it will just be alphabetical so it's best to only have 1 domain on "additional IPs", if they're owned. If the additional IP is shared, it doesn't matter, you'll be using the server's shared certificate anyway.
John