In short, you can’t. But there’s a work around.
Let’s say your company’s primary domain is www.PrimeWidgets.com and this is your primary domain in Google Apps. You’re sister company at www.SuperManufacturing.com will be handling sales generated from your secondary domain in Google Apps, www.mywidget.com. You want emails sent to the sales rep email@example.com as well as firstname.lastname@example.org to forward to email@example.com.
How’s that for a crazy ass setup? Yes I ran into just such a situation and so document the resolution for your purusal.
First, you have to setup a group for firstname.lastname@example.org that forwards to email@example.com.
Now your next thought is to add mywidgets.com as an alias of mywidget.com and be done with it; not so fast. As of this writting you can’t attache an alias domain to a secondary domain in Google Apps.
The fix is to add mywidgets.com as an additional secondary domain and setup an second group firstname.lastname@example.org forwarded to email@example.com.
It’s less that elegant, but will work until Google fixes an obviously, to me, missing feature.