Recommended softwares
To upload files on your web servers, you can use a simple FTP client. I recommend WinSCP or CoreFTP.
If you are using FileZilla and you are experiencing problems (corrupted files, or your game can't start), try to re-upload everything with a different FTP client. A lot of my customers experienced troubles and corrupted files while using FileZilla.
When distributing your Launcher to your users, you also want to perform some setup tasks the very first time a player opens the Launcher. An installer software can help you on this. I recommend InnoSetup and NSIS.
You can find an InnoSetup pre-configured sample for PATCH here.