I was however missing how one moves files to various directories.

If you by chance didn't move (with cd) to the correct directory
before uploading the file(s), you can use the mv command.

Like this:

mv myfile /drive0/var/

This will move the file myfile from wherever you currently are to the
directory /drive0/var/. You can copy (cp) or move a file from
anywhere to anywhere else. Remember that it is all one big filesystem
tree even if there are more than one partition/drive, and that you can
use full filenames (from the root: /drive0/var/myfile) or relative
filenames (let's say you're in /drive0; then you can use var/myfile ,
or if you're in /drive0/var/subdir - then you can use ../myfile)

/Michael