Request for help in rules setup.

Hello,
I'm hoping to get some help with the rules in Toucan.

I (currently) use Sync with the Mirror function to backup my files. The Source files are on a NAS so there is a large number of large files which necessitates (due to destination disk size limitations) syncing to different destinations. So I expect to end up with multiple Sync Jobs, each with a corresponding set of unique rules for the backups. And I would have a Script to run all of the jobs together.

The NAS files are mostly organised into sub-directories within the Source directory but there are some files that are not in sub-directories.

I thought I could have a set of rules similar to
Absolute Folder Exclude Simple *
Folder Include Simple Sub-1
Folder Include Simple Sub-2 etc for each sub-directory that job is to backup.

The final sync job would use
Absolute Folder Exclude Simple Sub-1
Absolute Folder Exclude Simple Sub-2 etc for each sub-directory that is in another sync job. This is so that if I create any new directories in the future they would automatically be included in my backups.

Now that does work (albeit a bit slow), but the problem I am experiencing is that all of the files in the Source directory that are not in any sub-directory; end up being included in every single sync job. So I end up with multiple copies in the different destinations.
I thought I could add
File Exclude Simple *
to the rules to prevent these files being included from most of the sync jobs but that doesn't seem to make a difference.

So my first question is - How do I exclude any file that not in a sub-directory from the sync?
And my second (less important) question is - Is there a more efficient way of defining the folder rules above to improve performance.

Thanking you in advance for any help offered.