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May 04, 2012 08:22 AM|LINK
Your web application and the web service project are two differents applications.
So you can deploy these two application seperatly on two differents vitual directory / application pool on IIS.
You need to create two differents methodes / Web deployment projects or something like that.
I don't understand why having already a web application would be an issue to deploy a web service. Could you maybe provide more information ? (Is it on IIS ? Which version ?)