Know-How Exchange : Branding

I am the editor of a magazine published by a charitable organization, and our organization is now re-working its logo and will have it approved very shortly. Other staff here feel that the organization's logo should appear on the magazine's letterhead, business card, etc. I agree that the magazine is a product of our org. and it should be identified as such, but instinct tells me that our product stationery should display the magazine logo, since that is what our readers and writers will recognize first -- it's what they paid to receive in the mail. The goal of a magazine editor is to create a virtual community among its readers, no matter where they are located, and I am worried that using the organization's logo first and foremost will confuse them and our brand won't be very strongly remembered. Our organization is a city-based organization and our readers are from across North America and they do not necessarily have any connection to the organization beyond the magazine. Before you answer, let me say that I *am* willing to indicate on the letterhead, etc., that the magazine is published by the organization, but I disagree that it's logo should be the most prominent. Any suggestions on what to do?