You send files through ssh using scp. The format is 'scp
user@original.address:/path/to/file
user@destination.address:/path/to/file'
You can use scp between two machines you are not even local to. However, when scp'ing from or to the local machine you are on you can leave out the user@address portion of the command.
If you will be transferring files between windows and nix you can pick up pscp for windows at the same site putty is hosted from.
G'luck