It's very easy to securely access your Linux server from a remote location. This howto discusses two remote accesss programs that run under Windows: PuTTY and WinSCP.
PuTTY is an ssh client that is run from a Windows box. It will provide you with a Linux shell on your remote server. This tool is all you need, there's nothing you can't do from the command line. But to make life easier, there's alsoWinSCP.
WinSCP is graphical directory browser, also run from a Windows box. It will give you remote access to the Linux file system, making it easy to edit configuration files with your favourite graphical editor.
Now you can locate your Linux server in a dark, out of the way closet. You'll rarely, if ever, need a keyboard or monitor.
(Both PuTTY and WinSCP require that an ssh server is running on the remote Linux box.)
Go here to download PuTTY. There's no install file, just the executable. Find a nice place to save it to, maybe C:\Program Files\putty\putty.exe. Put a shortcut in your start menu or on the desktop.
Go here to download WinSCP.