Bah so apparently the partitions weren't opened. So I used the command:
sudo cryptsetup luksOpen /dev/sdax name
where x is 5-8 depending on the partition and then in the manual partitioner they came up. I changed the mount points from /dev/mapper/root, /dev/mapper/home, /dev/mapper/usr, to /, /home, and /usr respectively. Then when I clicked next, a window came up saying
the file system on /dev/mapper/root assigned to / has not been marked for formatting. File systems use by the system (/, /boot, /usr, /var) must be reformatted for use by this installer. Other file systems (/home,/media*,/usr;local, etc.) may be used without reformatting.
Hmm does that mean I have to encrypt it after
I install and cannot make a fresh install to an encrypted partition? If so is there a command line way to copy the necessary image files and /root and then I guess find a list of programs to download?