Your phone number is just for reference, as far as your Lookout account is concerned.
You might still see your old phone number on Lookout.com, even if you've changed it for your device. This will not affect your Lookout services, however, as your account is principally connected to your Registered Email Address. The device stores the original number that it was activated with, and even if you change phone numbers the old directory will still be there. You can always run a test Locate and/or Scream to confirm that your Lookout services are still functional.
You may want to add a name to your device to help you identify it better. Instructions are available here.
Note: You may wish to contact your wireless carrier to update any data on the device so that it will reflect the new number.