Dave
There is alot in this topic.
For installation on multiple partitions, as you notice it is not really supported in the installer. It is seen as something more advanced users would have interest in and therefor know how to do so outside of the installer.
I have always formatted my drive the way I like prior to install using either parted or gparted.
Then boot into init level 3 by adding 3 boot kernel line in the boot loader.
Run the cli installer and install everything to a single root partition (aside from swap)
after cli installer finishes and before reboot make a temp mount directory (mkdir /mnt/temp)
run blkid id and place the output in /etc/fstab (blkid >> /etc/fstab)
edit the fstab file to make the proper mount specifications that I would like using the uuid’s that I sent to the file via blkid
manually mount every partition that I wish to have separate from root one at a time (mount /dev/sda2 /mnt/temp)
after mounting, run rsync with status=progress to make a mirrored copy of the directory in the / only install to the separated partition dedicated for that directory. (rsync /home/ /mnt/temp/ VARIOUS_RSYNC_OPTIONS_HERE)
unmount that partition (umount /mnt/temp/)
remove the files from the directory that I just copied to the dedicated partition. (rm /home/* -r)
repeat the previous 4 items for the other directories/partitions.
NOTE: if the boot partition is separated you would need to also install grub to the separated partition instead of the / partition.
shutdown the system, remove the live media, and boot into the main system.
If anything does not work, fix with the live media. I am not certain on encryption at the moment, it has been a while since I have done an encrypted installation.
Computers are like air conditioners. They work fine until you start opening Windows. ~Author Unknown