Do all FTP programs handle "overwriting" the same way gFTP and Filezilla do?

As an example:
If I have
Code:
folder/subfolder/one
                /two
                /three
allready on my website, with gFTP or Filezilla (the only FTP programs I'm familiar with) I can then upload
Code:
folder/subfolder/four
                /five
and though my FTP program will ask "okay to overwrite?" it doesn't actually overwrite any directories, it simply adds to them, so my end result is
Code:
folder/subfolder/one
                /two
                /three
                /four
                /five
Old AND new files all present and intact.

Is this how all FTP programs work?

I'm asking because I've got a template I would like to submit, and I'm trying to decide on the simplest way to explain installation.

Since the template has files in both
includes/languages/english/TEMPLATE
and
includes/templates/TEMPLATE
it would be easiest to just say "upload the includes directory to your ZenCart main directory". But if some FTP programs would then delete directories or files allready IN the includes directory... well... that would be horrid.

Thanks for any help!

-zami