"with-suexec-userdir" makes apache check the /home/directories for a folder called "public_html".
So users on the system can have their html pages served under their own username from http://localhost/~user/
This setup is more of a convenience to local users but is not as flexible as vhosts.
If you are running from vhosts the above mentioned parameters are not so relevant.
# suexec -V
For vhosts set AP_DOC_ROOT to "/websites/"
suexec checks if the vhost directory is underneith "AP_DOC_ROOT".
suexec checks if the vhost user/group matches ownership of the files in directory.
suexec checks if vhost user/group is not root or < 500/100