As far as I know, you can't do anything about the "one list" situation; I don't think you can avoid having all of your incoming messages grouped together. As far as the "sent from" problem, I'm able to choose whether my e-mail is sent "using" the "Desktop" (that is, the desktop redirector) or the web client. And my replies go through the particular service through which the original message is received. I'm not on a BES, but my (quite limited) understanding is that the same feature is available to BES users.
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