Google by the time of this writing is not accepting domain transfers neither mapping "naked" domains  which means I cannot host my external bought domain using either of these possibilities.
However if your domain account provider allows for URL Forwarding  like godaddy.com does then you can solve your problem as follows:
1. From http://appengine.google.com/ access your application to be mapped. Go to Versions, Add Domain. Click on "Sign up for Google Apps" Complete the form there (Remember your account admin information). Add your domain (for example nestorurquiza.com) and follow instructions in your email or from the web clicking on the link to verify your domain ownership. You might have to add a CNAME for your domain.
2. From your Google Application Engine Control Panel (in my case https://www.google.com/a/nestorurquiza.com) go to "Dashboard" "Service settings" "Add more services" and Enter your appId for "Google App Engine". Add as a Web Address "http://www..."
3. You might want to set up email delivery through Google. In order to make Google your email host follow the steps from "Dashboard|Set up Email" adding the proper MX records as directed there.
4. From your provider DNS admin page (godaddy.com for example) create a CNAME record for www (CNAME www ghs.google.com)
5. Your app should be accessible from www. now. So go to your provider DNS admin page and forward http://your-domain to http://www.your-domain
6. After some minutes your site will be accessible both from naked (just FQDN) domain (http://nestorurquiza.com) or www domain (http://www.nestorurquiza.com)
7. You can configure email, domains and more from your partner page (in my case http://partnerpage.google.com/nestorurquiza.com)