You are not saying what your "mail" command is... So I will have to guess.
For example, on most of my systems, "mail" is a simple SMTP relay, not a mail reader...
My guess: the "mail" command you refer to is based on unix accounts, you seem to be using a virtual mail system with one unix account and many virtual mail accounts so this will not be possible without some work. Other clients like courier-imapd/courier-popd support this out of the box, but I very much doubt that any command line email reader will.
One hack that might work would be to create symlinks to all the "/new/" (and "/cur/" if you want read mail too) directories from "/home/vmail/new/" named after each account it is for. You could also automate this:
- /home/vmail/site_com_username -> /home/vmail/site.com/username/new/
- /home/vmail/site2_com_user2 -> /home/vmail/site2.com/user2/new
That is your assuming your current "mail" command looks for mail in "/home/vmail" (dubious - often they look for a ".maildir" mailbox) and that it understands mail subdirectories. If not, then get one that does support this.