If you're just using the 36Gb drive for backup there is ABSOLUTELY nothing to worry about. Just format the 36Gb drive with SFS and leave your other drive alone. Backup everything to the 36Gb drive and leave it at that.
...But I'm sure once you use SFS on the 36Gb drive you'll realize that all your fears are unfounded and want to switch your SYS partition to it as well.
And don't worry about having a spare "bootable" partition. Any partition can be made bootable at any time. Just go into HDToolBox and select "bootable". It doesn't change any data on your drive.
What I would do is:
Say you make a 36Gb SFS partition called BU0: and SYS: is on a partition called Workbench:
Copy Workbench:#? BUO: all
Go into HDToolbox and make BUO: bootable with a higher priority than SYS:
change Workbench: to SFS
reboot (you Amiga should automatically boot off BUO: and everything will look EXACTLY like it did before)
reformat the Workbench: partition
copy BU0:#? Workbench: all
go into HDToolbox and deselect "bootable" for BU0:
simple as that.
