The fastest way to upload the Magento files via FTP is to upload the tar.gz distribution and untar it via SSH. This should maintain the integrity of the system files and folders.

First upload the files to the desired location on your server. For example, if you wish to have your store at www.domain.com/magento/ simply upload your tar.gz file to the web root, as the files will be automatically untarred into /magento/. If you want to have your store at www.domain.com/store, do the same thing, and after the files are untarred, simply change the /magento/ directory to /store/. If you wish to have your installation at the web root (accessing the system via just www.domain.com) you can move all the files inside /magento/ to be at your web root.

In order to untar the files:

1. Login via SSH (using an SSH tool such as Putty).
2. Browse to your directory containing the tar.gz using the following command: cd /path/to/tar/file/
3. Use the following command to untar the file: tar -xzvf magento.tar.gz

Enjoy!

See also Magento-Installation-via-SSH