The instructions Google provides are quite simple. All you need to do is update the MX records for your domain with the following:
- ASPMX.L.GOOGLE.COM. (Priority: 10)
- ALT1.ASPMX.L.GOOGLE.COM. (Priority: 20)
- ALT2.ASPMX.L.GOOGLE.COM. (Priority: 20)
- ASPMX2.GOOGLEMAIL.COM. (Priority: 30)
- ASPMX3.GOOGLEMAIL.COM. (Priority: 30)
- ASPMX4.GOOGLEMAIL.COM. (Priority: 30)
- ASPMX5.GOOGLEMAIL.COM. (Priority: 30)
GoDaddy even provides a wizard [dead] to do this, which is where things can go wrong. The wizard only works if you have your domain's DNS hosted with goDaddy. If you have your Name Servers pointing elsewhere, like your hosting provider, your MX records will remain unchanged and google apps setup will continue to report "Updating (May take upto 48 hours)" indefinitely.
Instead, you need to update the MX records at wherever your Name Servers are pointing. Most likely in your hosting company's control panel. It makes perfect sense, but if you're doing things in a hurry it's easy to make the mistake.