I have used this great tutorial to install BackTrack 5 with full disk encryption on my laptop:
I preffer to have BackTrack 5 bootable from my USB disk also if I need it.
And I need it if I do any update to grub or certain packages in BT5, so I preffer to have this set of commands handy to fix issues with my encrypted partition.
You just have to boot BackTrack 5 from LiveCD / USB and do the following:
/etc/init.d/networking start apt-get update apt-get instal hashalot cryptsetup luksOpen /dev/[your logical partition] pvcrypt mkdir /mnt/bt5 mount /dev/mapper/vg-root /mnt/backtrack5 mount /dev/[boot partition] /mnt/backtrack5/boot mount -t proc proc /mnt/bt5/proc mount -t sysfs sys /mnt/bt5/sys mount -o bind /dev /mnt/bt5/dev chroot /mnt/bt5
Once you are in chroot-ed enviroment of your encrypted drive now you can do for example GRUB update.
After you are done, you can just reboot. If you still can not boot into BackTrack, repeat the steps and try to figure out what step went wrong.