Kevin reidy: When you download the ThingWorx installer from PTC Software Download portal then there is a zip file that is provided. e.g. sample MED-61111-CD-080_SP1_ThingWorx-Platform-XXXXXX-X-X-X.ZIP . If you unzip this file, you should be able to see the Thingworx.war file inside the unzipped folder along with install & update folder.
Once you have this file, you can deploy it using Tomcat Manager or place it under your tomcat directory ( Tomcat\webapps\).
Hope it clarifies and let us know if you still have issues.