There is no "magic" in either Eclipse or the sysdeo plugin, so nothing will automatically be detected as a webapp. Which is actually the way I like it. I build my webapps in a project directory named build/webapps, which is the directory I zip up when I create a WAR. Tomcat can be instructed to look there - all I have to do is add a context file to TOMCAT_HOME/conf/Catalina/localhost that points to that directory.
If I was using Maven, Maven has its own ideas on project directory layout. Eclipse and the sysdeo/tomcat combo are equally willing to work with Maven's idea of build directory structures.
An IDE is no substitute for an Intelligent Developer.