hi malikawan,
i also use boot code "protect" and the required password substitutes my user password at every boot.
confidential files and data are stored in an encrypted file-container that is secured by an additional password and this file-container is only opened by request, when these encrypted files are really needed :-)
i use cryptsetup with a file-container that is mounted by a loop-device:
$DB is my mount-point
$DATABOX is my file-container
sudo mkdir -p /mnt/$DB
sudo mknod -m 660 /dev/loop256 b 7 256 > /dev/null 2>&1
sudo losetup /dev/loop256 $DATABOX > /dev/null 2>&1
sudo cryptsetup luksOpen /dev/loop256 $DB
sudo mount -t ext3 -o rw,defaults /dev/mapper/$DB /mnt/$DB
this solution can be used on different linux-platforms without any changes...