Magento backup problem

Sorry for two posts in a row but I think you didn’t see my second edit so here I post it again:

So as I thought I ran into problem with denying access. I tried to upload a logo and again I had to create directories manually via FTP and even after Magento can’t copy the logo (and doing it manually won’t work for some reason). I get this:

The file or directory "/var/www/html/pub/media/tmp/design/file/logo_4.png" cannot be copied to "/var/www/html/pub/media/logo/stores/1/logo_4.png" Warning!copy(/var/www/html/pub/media/logo/stores/1/logo_4.png): failed to open stream: Permission denied

So my question is did you ever ran into similar problem or perhaps know a solution to this? I have all the permissions set in user roles, I made another user, same problem. Don’t know what to do.