Hi Nicky,
yes inside server there is classes, lib and webapps. both classes and lib are empty for me, but webapps has manager as a subdirectory and then the normal directory heirachy under it, for a web application.
If you haven't created any webapps you can just uninstall
tomcat and reinsatll it if you are not sure about things. If you have created webapps then just copy the c:/Tomcat_5.5/webapps directory somewhere else uninstall, reinstall and copy the webapps directory back. You will get the copy asking you if you want to replace files, say no, just copy the files that don't already exist and it should all work again.
good luck
HTH
Mat