You could give this a try in your .btdfproj:
This is completely untested, but it seems like it should work...
Thanks,
Tom
<Target Name="Deploy2ndWebService" AfterTargets="DeployVDirs">
<CreateProperty Value="IIS://localhost/w3svc/2/Root">
<Output TaskParameter="Value" PropertyName="IISMetabasePath" />
</CreateProperty>
<CreateItem
Include="*" AdditionalMetadata="Vdir=MyVDir;Physdir=..\OtherWebService;AppPool=DefaultAppPool">
<Output TaskParameter="Include" ItemName="VDirList"/>
</CreateItem>
<CallTarget Targets="DeployVDirs" />
</Target>
The idea being that the normal built-in process runs first, then this custom target runs. It overrides the IISMetabasePath and VDirList, then calls DeployVDirs again but this time the new values should be in effect.This is completely untested, but it seems like it should work...
Thanks,
Tom