I am trying to deploy to tomcat5. The server is pointed to the correct installation directory in
window->preferences->myeclipse->application servers->tomcat 5. I try to deploy to tomcat 5
and i try to add a deployment and the app is placing it in webapps/ROOT, not webapps.

Stacey,
If you open up your project properties, and go down to MyEclipse-Web, the 2nd field "Web Context-root" should be something like /myapp. If it's just a slash (/) then it will deploy your app to the ROOT context so you can access it like:
http://localhost:8080/index.jsp