FTP and wp-admin differ and/or don’t reflect one another.

I have been trying to add favicon and image to sidebar via FTP. However I am using punchcut and to use a Child version I had to upload a zipped file via the wp-admin page online rather than my FTP as the changes are not reflecting on either one. How can I get changes I make to my FTP reflect on my wordpress site/admin?

Thanks,
Josh