Hi
The first root u are talking about is the servlets directory under the Server Root.U can use this place to put the servlet classes , which generally are not to be reloaded.
While invoking the servlet the following type of URL need to be used.
http://host/servlet/package.servletclass U need to invoke the servlet using full class path.
If u want to invoke the servlets by alias name, if u need to reload your servlets, want to supply initialization parameter,
want to preload your servlets or want the WAS security to secure the servlets then u need to put the servlets in the web application class path.
The URL to invoke the servlets within the web application is as follows:
http://hostname/webapp path/servlet(alias name).
Hope this clarifies your doubt.
regards
Ram