For those of you who want to use Google Analytics or Webmaster tools, you can do that, directly through Cloudflare.
Step 1: Login to Cloudflare
Step 2. In the control panel, under the site you want to manage, select the Apps icon
Step 3: Scroll down and select setup on the app you want to install. In this case Google Webmaster Tools.
Step 4: Click start to select which account you want to use.