We do not recommend to update the Eclipse platform version using the standard Eclipse update mechanism, but instead to start with the fresh installation of STS 3.6.0. You can continue and use your existing workspaces with the new version. But keep in mind that once such a workspace is used with Eclipse 4.4, it is broken for older Eclipse versions. So keep a backup of your workspace before testing the new STS version, I think.
If you have a lot of additional plugins installed, you might also be interested in using a script to batch-install additional plugins from the command line instead of walking through the "Install New Software" UI several times. Here is a such a script: https://gist.github.com/martinlippert/5155155. It is built for OSX, but I am sure you can port that to Windows or whatever.
If you wanna give the update mechanism of Eclipse a try, you can also try to upgrade your existing installation to Eclipse 4.4 by adding the STS and the Eclipse update sites for Eclipse 4.4 in your preferences. But again, I would expect a lot of hiccups and issues while doing this.