Abhi,
The configuration center is no longer present in MyEclipse 2013, features provided by it have been replaced. For more details on these changes, please read Delivery Changes in MyEclipse 2013 – http://www.myeclipseide.com/images/tutorials/me_2013/delivery_changes/
You can add subclipse plugin from Eclipse marketplace. Go to Help > Install from catalog, Eclipse marketplace opens up, search for subclipse plugin and click on install button and follow the wizard.
Alternatively, you can install subclipse plugin using this update site – http://subclipse.tigris.org/update_1.8.x
> Go to Help > Install from site
> Click on Add, add the name and the above url in the Add repository window and click ok
> Select the plugin you wanted to install and click Finish and follow the wizard.
Let us know how this works for you.