MS SOAP Toolkit generates rpc/encoded by default, but you can manually modify the generated WSDL to make it support document/literal. In any case, you shouldn't use MS SOAP Toolkit any longer. Microsoft terminated support for the product in April 2005.
Microsoft provides utilities that allow you to use .NET SOAP support with COM-based systems. See this article for more details.
As an alternative, you should consider using PocketSOAP, which provides a state-of-the-art SOAP platform for COM.
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