I use Google apps for my business, as a paid user its the only way to go for my purposes... I did get a reply back from Google support that I will include here for anyone that cares:
Hello Jesse,
Thanks for your message.
At this time, you will not be able to purchase apps from the Android Marketplace using your Google Apps email address. We are currently working on a solution to this, that will be coming out in the following weeks.
I would like to point you to our blog
http://googleapps.blogspot.com to get up to date information regarding this. You can sign up for the RSS feed or email updates also if you please.
I am sorry for any inconvenience this may have caused you, and I hope that you have a little more patience while we implement a solution in regards to this.
Sincerely,
Jim
Enterprise Support