MSDeploy will use the physical location of the web site that the web application is being deployed under, if you're deploying a web application without specifying a physical location in the parameter settings.
Specifically, MSDeploy uses the physicalpath attribute for the site defined in the applicationHost.config file, which is located C:\Windows\System32\inetsrv\config.
So for example, my default web site is defined as physicalPath="E:\inetpub\wwwroot", which is specified in the virtualDirectory element. I have an application whose virtual path is under the default web site. When I deploy this application, which doesn't have a physical location specified as a parameter, it will use E:\inetpub\wwwroot as the base, and create a sub folder - e.g. E:\inetpub\wwwroot\NewApplication.
One thing to keep in mind, once the deployment has been performed, a new application element is created in the applicationHost.config file for the web application deployed. If you delete the application from IIS - the configuration remains for the application. This is key to remember, as this will now become the default physical location for the application, regardless of the physical location of the default web site. So if you want MSDeploy to use the default web site's physical address as the base address (assuming your deploying your applicaion under DWS), then you'll have to manually delete the application element for the web application in the applicationhost.config file before executing the deployment.
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