To add a domain, do not use the VqAdmin link from your machine's web interface. It's been depreciated and may cause unexpected results. Instead, use the command line.
To add a domain, use this command:
/home/vpopmail/bin/vadddomain -q 15000000 testdomain.com newdomain
This creates a new domain called "testdomain.com", with a quota (for postmaster) of (roughly) 15M (you have to define the postmaster quota in bytes) and a password of "newdomain" for the postmaster account. This gets the general framework set up for the domain. Now lets finishing configuring it:
/home/vpopmail/bin/vmoddomlimits -P 100 -A 100 -F 100 -R 100 -L 100 -q 15000000 testdomain.com
This sets some limits on the domain so the person managing it doesn't run rampant. I'll run through the limits in order. The -P flag allows the domain to have up to 100 POP accounts. The -A flag allows the domain to have up to 100 aliases. The -F flag allows the domain to have up to 100 forwards. The -R flag allows the domain to have up to 100 autoresponders. The -L flag allows the domain to have up to 100 mailing lists. Lastly, the -q flag sets the quota (max mailbox size) for each user - it's defined in bytes, so 15000000 is roughly 15M. There are additional flags you can set to add other restrictions to domains. Check out the vmoddomlimits page for more info.
That's roughly it. You now have a domian called "testdomain.com" that can have up to 100 email accounts, with 100 aliases, 100 forwards, 100 autoresponders, 100 mailing lists, and each user can have a mailbox of 15M.