The following is from the link to the Configuring Qmail site I gave above...
By default, Qmail is set up to put incoming messages into [tt]$HOME/Mailbox[/tt]. So a user [tt]joe[/tt] would get his incoming messages stored in [tt]/home/joe/Mailbox[/tt]. I don't like this default location, I want messages to go into [tt]$HOME/mail/inbox[/tt] instead, so I made these changes. If you want to use the default [tt]$HOME/Mailbox[/tt] file, you can ignore this section. Note that Qmail also supports a Maildir format, read the Qmail docs for more information.
[tt]/etc/qmail/dot-qmail
| dot-forward .forward
./mail/inbox[/tt]
The [tt]dot-forward .forward[/tt] command tells Qmail to forward emails if a .forward file exists in a user's home directory.
The [tt]./mail/inbox[/tt] line tells Qmail to store incoming messages in [tt]$HOME/mail/inbox[/tt], so if your username was joe, your incoming messages would go into [tt]/home/joe/mail/inbox[/tt].
[tt]
/etc/profile.d/qmail.csh
/etc/profile.d/qmail.sh
[/tt]
These files define the MAIL and MAILDIR environment variables. Some programs, such as mailx and the shell, look at these variables to see where your inbox is. Change all occurrences of [tt]$HOME/Mailbox[/tt] to [tt]$HOME/mail/inbox[/tt].
You may also want to check your [tt]/etc/profile[/tt] file to see if it defines MAIL. If so, you can remove the declaration because they are overwritten by the declarations in [tt]/etc/profile.d/qmail.csh[/tt] or [tt]/etc/profile.d/qmail.sh[/tt] (depending on which shell you are using).