This should be fine (this is how I use it too :) It will keep your preferences for each Gmail account (for example, you can have different Smart Lists displaying in each account). Hope this helps!

I was doing this very same thing for the last two weeks and loving it! This morning for some reason. RTM for gmail now only works with my personal gmail account, not my work GAFYD account. I've reinstalled RTM, I've tried logging into one account and not the other, etc... I've exhausted every other possibility. Any ideas are greatly appreciated. Thanks.
Chad.

I'm seeing this same behavior. It worked for me previously as well. I need it back!!! Great service.

Yay! I found it. There's a little triangle just to the right of my email list (ex. Inbox page). Clicking that triangle opens up the RTM window. I don't know why it was automatically closed all of the sudden. I didn't even notice it would do that. Good to know.

Everything is good now. :-)