1. How should I start qmail, smtp and pop to create the right kind
   of logs?

First make sure you have the log directories:
mkdir /var/log/qmail
mkdir /var/log/pop3
mkdir /var/log/smtp
chown qmaill /var/log/qmail
chown qmaill /var/log/pop3
chown qmaill /var/log/smtp

Then start up qmail

        env - PATH="/var/qmail/bin:/usr/local/bin" \
        qmail-start ./Maildir/ | /usr/local/bin/setuidgid qmaill \
        /usr/local/bin/multilog t n100 s1000000 /var/log/qmail &

        env - PATH="/var/qmail/bin:/usr/local/bin" \
        tcpserver -v -H -R -l$HOSTNAME -c200 0 110 /var/qmail/bin/qmail-popup \
        $HOSTNAME \
        /home/vpopmail/bin/vchkpw /var/qmail/bin/qmail-pop3d Maildir 2>&1 |  \
         /usr/local/bin/setuidgid qmaill \
        /usr/local/bin/multilog t n100 s1000000 /var/log/pop3 &

        env - PATH="/var/qmail/bin:/usr/local/bin" \
        tcpserver -v -H -R -l$HOSTNAME -x /home/vpopmail/etc/tcp.smtp.cdb \
        -c200 -u8002 -g8001 0 25 fixcrio /var/qmail/bin/qmail-smtpd 2>&1 | \
        /usr/local/bin/setuidgid qmaill \
        /usr/local/bin/multilog t n100 s1000000 /var/log/smtp &
 
2. My logs are not in the places above, what should I do?

Edit qmail.mrtg.cfg and changes the lines like:

Target[messages]: `/usr/local/bin/qmailmrtg7 m /var/log/qmail`

To point to your log directory. In the above line the log
is in /var/log/qmail, you might have it in /var/log/qmail/qmail-send.