FTP is just not secure by itself. So if you value your server’s securely you simply won’t use it for uploading or editing your site. We highly recommend a program like WinSCP, http://winscp.net/eng/index.php, to upload or edit your site. WinSCP can use your editing PuTTY key pairs with SSH to get to your server. This is MUCH more secure, and you never expose your password.
We do recommend that you make changes to you site’s files on your local machine and then upload them (with WinSCP) all at once. But what if you need to make a change on the fly? Sure you could log in with PuTTY and use vi,vim, nano, or one of a dozen other editors. But WinSCP can help you out there too. You can use your existing Windows based editor with WinSCP. Personally, I love EditPlus, http://www.editplus.com/, it’s small fast and has a lot of features. But it doesn’t work over SSH (at least not last time I looked anyway).
First, setup WinSCP to get to your server like you normally would. It will need the FQDN or ip address, port number (you’re not using 22 anymore right?), your login, and your key file. Go ahead and save the session… Now on the left side tree menu, select Preferences, and then select the Preferences… button, and a new window should appear with new left side tree navigation. A few down, there is a leaf called a Editors, select that. It should look like this:

Click the Add button. Select the External Editor radio box, then click Browse. Find the path to your editor, in my case that was c”\Program Files (x86)\Edit Plus 3\editplus.exe - you’re may be different depending on OS version and what program you want to use. Under editor autoselection, you might want to change the association, say EditPlus for php files or .conf files. There’s another option there too… Inside the Add dialob box, there’s an “Associated Application” – then specify the type of files you want opened with your default Windows application for that extension. For example, I use CorelDraw for .cdr and .psd files, and Windows will automatically open CorelDraw for me if I double-click in Explorer. With the Associated Application radio box, that is extended into WinSCP as well. So inside of WinSCP if I double-click a .cdr or .psd file, CorelDraw opens automatically, and when I click save it is transferred back to the server. This is even great for using different types of editors for different files.
You probably need to change the order in which programs are checked in the list. WinSCP goes from top to bottom until it finds an editor it can use for the file. So I’d put “Associated application” at the top, then your prefered text editor(s), then WinSCP’s internal editor at the bottom.
Sometimes, you’ll have issues with backup copies that programs make, or you may just want to keep them saved locally… Sometimes this is easily accomplished. For EditPlus, go to Preferences, then Files. There is a checkbox called “Create backup file when saving”, check it if it’s not. Then hit the button next to it “Backup Options”, select your local backup directory, and check the “Create backup file of remote file in backup directory” box. And you should be good to go.
Caution… As with any changes to a system, before you use this for real (ie a real configuration file that matters to you), create a dummy file out in a directory you don’t care about, and TEST it. Make some changes to that file. Check that it works as you expect BEFORE using this for real production files. Of course, best of all is to not use this on production files directly, but to edit them locally then transfer when you’re sure they’re right, but as you know life doesn’t always work that way.