What is the right way to get XML commands to the JobScheduler (presumably the JobScheduler web service)?
One method for forwarding XML commands to the JobScheduler is described in: Automatically Generating Jobs and Orders
A possible alternative is the creation of XML files and putting them in the live-folder. Which alternative you choose depends on the persistence required of the JobScheduler objects. All objects in the live folder are persistant, objects created by the external API (XML commands) are not.
Regarding the JobScheduler "WebService": you are able to use the service to send some - but not all - commands as SOAP requests to the JobScheduler but note that there is no WSDL and the JobScheduler itself is not aware of the webservice. There will be a conversion based on XSLT for incomming and outgoing SOAP messages. These XSLTs have to be adjusted to your requirements. If you do not really need to use SOAP messages, it will be more efficient to use TCP/IP or HTTP instead.