This is in response to an email I got from Edgardo (www.geekswithblogs.com/evega), I post it here hoping it will benefit more people out there.
You can call a webservice from inside a workflow in Siebel, and you can have a webservice that starts a workflow. The first thing I do is test the webservice using XMLSpy Enterprise (Pricey but well worth it, and saved me a lot of time). XMLSpy will generate the test SOAP message for you, and you can override the parameters to make sure you test all the cases with the webservice.
Once you are happy with the tests copy the link to your Visual Studio BizTalk Project, select add a web reference, insert the url in the address line, and check the webmethod(s) that come back, they will be the same ones detected by XMLSpy . Once you have added the webReference, create and orchestration that calls it. If you create the ports in the orchestration and you select "Specify Now" rather than "Specify Later" then the url settings for the webservice included in the wsdl will be used. This is the url that the Siebel workflow developer assigned when he/she generated the wsdl (Siebel has a wizard for doing that). When you deploy your application, BizTalk will create your SOAP send port with that url in it. If you Choose “Specify Later” then you will have to create the port(s) manually or using script.
I hope this helps and good luck.