Situation:
I have a directory (say source/) with many sub directories and files under it (source/dir1, source/dir2, … , source/file1, source/file2, …). I want to copy it to two separate folders (say destA, destB). The first folder contains all the top level files (source/file1, source/file2 etc.,), the second folder contains the rest (source/dir1, source/dir2 etc., but not source/file1, or source/file2 etc.,).

Solution:

rsync -prltvzD -n --delete-after --exclude='/*/' source/ destA/
rsync -prltvzD -n --delete-after --include='/*/' --exclude='/*' source/ destB

• https://linuxize.com/post/how-to-exclude-files-and-directories-with-rsync/ - shows how to exclude files and directories with rsync; goes over many cases with examples and simple explanations.