just to make some things clear..There is nothing like different servers provide different deployment hierarchy...For any j2ee complaint server,they need to implemet the spec by sun..But they can provide extensions on top of existing deployment hierarchy...
Ex:Some of the xmi files which IBM app server has in its web deployment hierarchy..
but tomcat is really simple and eclipse has it as an integrated server.So you can just deply/develop everything from IDE.
I never tried working out examples as i had prior experiance but if you are new,its better to have installation environment.
Hope This Helps