FTP do have two modes: binary and ASCII. By default most clients use ASCII mode, which breaks your binary files completely. I don’t know which FTP client you are using, but for example in ncftp you can use command “binary” to switch to binary mode.
If you want to create ZIP files using Ubuntu (or almost any other Linux), use
zip. You can install it to Ubuntu by running
sudo apt-get install zip
Then you can create zip file by running
zip -r compressed_filename.zip foldername UNZIP
If you want to extract to a particular destination folder, you can use:
unzip file.zip -d destination_folder