correct way to customize rwd theme ce 1.9

If you haven't seen it already, check out http://www.magentocommerce.com/knowledge-base/entry/ee114-ce19-rwd-dev-guide.

The guide has additional information you'll need to get started.

If you want to Customize RWD theme.in your rwd package you can make a new theme like

design/frontend/rwd/yourtheme and start copying the files which you want to customize in yourtheme.

copy files from design/frontend/rwd/default to design/frontend/rwd/yourtheme and start customization.