I have not done a lot of work with this web interface since I have a small user base and customization of the web interface is not necessary. Off the top of my head I can think of two different ways to accomplish this.

Install the web interface once, then use IIS Host headers to set different host names (IIS Manager -> Web Sites -> Your Web Site Name -> Right Click -> Properties -> Web Site Identification -> Advanced). Note: Instructions are for IIS6 on W2K3, newer or older version of IIS may be different. See image at right.
The second method would be to install the web mail on each web site, but to me that is a bigger maintenance issue when you need to upgrade the web interface.
I also recall the new version of the web interface supporting themes. Please see the following ArGoSoft Document on the subject:
Title: How to Change the Theme According to the HOST HTTP Header
URL: http://www.argosoft.com/RootPages/MailServerNET/Documents/WebInterfaceThemes.aspx