Use this idea ^ but add Multiple Inboxes from Gmail Labs. Forward your google app domain emails to your main gmail account and add a filter to apply a tag and r

Use this idea ^ but add Multiple Inboxes from Gmail Labs. Forward your google app domain emails to your main gmail account and add a filter to apply a tag and remove it from the inbox. Set your top inbox to only show emails with your googleapps tag. It may be enough of a separation for you but you will have to forward all your emails ;(