When you want to edit an existing layout you will start off in the layout or preset manager and select the CSS Sculptor Layout you want to change, then click edit. When the Sculptor interface appears you will select to customize the css. When you customize the preset from here and click on finish you should have the ability to save over the existing preset or create a new preset based on your edits.
Does this option just now show up for you when you after you edit an existing preset? Do you get this option to appear when you create a new layout from within CSS Sculptor? Please post back with this info so we can determine how to proceed.