Sorry to resurrect an old thread, but I have a similar problem and hopefully you can help.
I use Gmail as my primary email, but I also have a Google apps account that is forwarded to my Gmail (the settings to forward are not set up through Gmail). On the computer, I have it set so that I can compose a new message and change the from field to be either from my Gmail account or my Google apps account. This way I keep everything in my Gmail account (so I can search for both sent and received messages later) but make use of both email addresses.
On my Droid X, I set up both accounts in the Gmail app. Now, from within my Gmail account, I can compose a new message from either my Gmail or Google Apps account. That part is good, but the same functionality does not carry over to replying to messages. If someone sends a message to my Google Apps account, I receive it in Gmail but when I hit the "reply" button I can only send from my Gmail address. Is there a way to reply, from within Gmail on my Droid, from the Google Apps account?
On the computer, "Reply from the same address the message was sent to" is checked, but it doesn't seem to carry over to the Droid version.