When we add a field to the site content type SharePoint doesn't push-down those changes to the document library and the list level. The below code sample is for push-down all the changes to document libarary and the list level.The sample code from WSS 3.0 SDK doesn't seem to be working :) 

SPField field = spWeb.Fields[“YourNewField”]; //you can pick one from the site column collection for create a new one.

SPFieldLink fieldLink = new SPFieldLink(field);

SPContentType contentType = spWeb.ContentTypes[“Site Level Content Type”];

contentType.FieldLinks.Add(fieldLink);

contentType.Update(true);