Putty is a free program that is used by a lot of developers to manage their servers through command line.
It offers a lot more, but it's key feature is that it allows you to us SSH to securely connect directly into your server. In order to this you will normally need root access to actually do any changes.
To get putty you can download it by click here. Or you can go to the main website of putty at: http://www.putty.org/. I know the site might not look like it should be trusted, but it actually is the official site for putty.
Once you have downloaded it you won't need to install anything. You simply run the program directly from the file you have downloaded. This makes it very portable if you was to put it on a memory stick.
Once you open the program you will see a screen like this:
Simply enter you server IP address and make sure SSH is selected.
Once you have done this click open. This will then open a new terminal window and ask you for username and password.
Normally this will be root for the user. Then it will ask for a password, please note that when typing the console won't show anything at all.
Tip: You can copy text from you computer into the command window by selecting your text and pressing ctrl+c then clicking back into your window and right clicking. This is very useful for super strong passwords, which should have!
Once you have logged in you are now ready to do what ever you need to do.
If you have a new server then you might want to install a LAMP stack.