Quelli che trovi di seguito sono degli appunti di una procedura che utilizzavo per il chroot di Apache qualche tempo fa.Dovrebbe essere ancora valida,vedi se riesci a ricavarne qualche spunto utile per la tua configurazione. 
Codice:
# vi /etc/apache2/apache2.conf
PidFile /var/run/apache2.pid
ChrootDir /var/www/apache
LoadFile /lib/libgcc_s.so.1
LoadFile /lib/libnss_dns.so.2
#ServerRoot "/etc/apache2"
mkdir -p /var/chroot/apache/var/www
cd /var/chroot/apache
mkdir bin dev etc lib tmp usr var
mount -t auto -o bind /var/www /var/chroot/apache/var/www
mount -t auto -o bind /tmp /var/chroot/apache/tmp/
cd /var/chroot/apache/usr
mkdir bin lib sbin share
cd /var/chroot/apache/share
mkdir curl misc php
mount -t auto -o bind /usr/share/php /var/chroot/apache/usr/share/php
cp -a /etc/mime.types /var/chroot/etc/
cp -a /usr/share/zoneinfo/Europe/Madrid /var/chroot/usr/share/zoneinfo/Europe/
cp -a /etc/adjtime /var/chroot/etc/
# vi /etc/fstab and add mount points
/var/www /var/chroot/apache/var/www auto bind 0 0
/usr/share/php /var/chroot/apache/usr/share/php auto bind 0 0
/tmp /var/chroot/apache/tmp auto bind 0 0
cd /var/chroot/apache/var
mkdir run cache
mkdir /var/chroot/apache/var/cache/apache2
chown apache:root /var/chroot/apache/var/cache/apache2
chown -R www-data:www-data /home/www/var/www/
cd /var/chroot/apache/var/run
mkdir mysqld
chown mysql:mysql /var/chroot/apache/var/run/mysqld
cd /var/chroot/apache/lib
cp /lib/ld-linux.so.2 .
cp /lib/libc.so.6 .
cp /lib/libdl.so.2 .
cp /lib/libncurses.so.5 .
cp /lib/libnsl.so.1 .
cp /lib/libnss_compat.so.2 .
cp /lib/libnss_dns.so.2 .
cp /lib/libnss_files.so.2 .
cp /lib/libnss_nis.so.2 .
cp /lib/libz.so.1 .
cd /var/chroot/apache/etc
cp /etc/hosts .
cp /etc/ld.so.cache .
cp /etc/localtime .
cp /etc/nsswitch.conf .
cp /etc/passwd .
# vi passwd (leave bin, mail, postmaster, nobody and apache)
cp /etc/resolv.conf .
cp /etc/services .
cd /var/chroot/apache/dev
mknod -m 444 urandom c 1 9
mknod -m 666 null c 1 3
cd /var/chroot/apache/bin
cp /bin/sh .
# vi /etc/mysql/my.cnf
[client]
socket = /var/chroot/apache/var/run/mysqld/mysqld.sock
[server]
socket = /var/chroot/apache/var/run/mysqld/mysqld.sock
/etc/init.d/mysql restart
# make sure you're env knows to where it's at.. simple create alias
vi /root/.bashrc
alias mysql="mysql -S /var/chroot/apache/var/run/mysqld/mysqld.sock"
Errore : Please verify that the current setting of session.save_path is correct
Soluzione :
# vim /etc/php5/apache2/php.ini
#MODIFICATO PER MOD_CHROOT APACHE
;session.save_path = /var/lib/php5
session.save_path = /tmp
ae2nmod mod_chroot
apache2ctl stop
apache2ctl start
# vim /etc/apache2/envvars
export APACHE_PID_FILE=/var/www/apache/var/run/apache2.pid
#export APACHE_PID_FILE=/var/run/apache2.pid
/etc/init.d/apache2 stop
/etc/init.d/apache2 start
Segnalibri