I'm not a fan of the SFFS interface - I agree its poorly designed in terms of user interaction.
In terms of setting up a backup, if you simply go through everything you *should* be covered
Saying that I have been caught by an overlooked setting -
which can be easy to do cause it takes a while to follow/understand it all - I've found
Generally I copy a Profile I'm happy with for a new profile & work from there
I generally start scheduler manually each morning -
I dont
want it running till i start working
but
I'm sure the scheduler works - worked for me before anyways -
Options: restore previous windows & scheduler states. should cover you?
That with having to disable scheduler I've gotten used to

By default SFFS insists on zipping each file individually - expect fun manually unzipping thousands of files, one by one, if you ever need to access the backup without SFFS!-tranglos

eh,
with winrar at any rate I just select the zip files I want to restore (edit: i.e. all selected same time!)
right click - extract here
& the original folder hierarchy is recreated
In fact for restoring a lot of files I find it a very good solution
I have restored stuff - from one folder - but not to original folders, & found it so easy I havent even used SFFS for it
Copying to original location then should be no problem too
I guess if you want to restore a whole bunch of stuff from different folders you'd need to use SFFS
Also, I've personally had no problems extracting encrypted zip files with Directory Opus and Win Explorer
Tranglos, have you tried DirSync ? (see post #13) I havent but if
you've tried everything else...

PS/EDIT: just noticed, on my system SFFS is using 10MB memory if I'm reading correctly (private bytes - Process Explorer)