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To convert partition,s to the ext3 filesystem, you need to cleanly unmount them, boot something else (like the Debian CD you installed from -- see Section 6.2 on how to do this), and then, on a console, do:
tune2fs -j /dev/hdaX
wherein /dev/hdaX is the partition you want to add journaling to (hence the `-j' flag).
Don't forget to modify the lines in your /etc/fstab to reflect that the partitions in question are to be mounted as ext3, not ext2. When cleanly unmounted, they can still be mounted as ext2, but the whole point of changing them was so they wouldn't be.
That's it. When you reboot, your partitions should come up as ext3.