I think the best thing to do is to get your development environment setup first; set up the directories, libraries etc. Configure your classpath. Then compile everything, create a war file (or an ear file), deploy it in Tomcat.
For a next development cycle, repeat the above steps; change code, compile, create war file, deploy to Tomcat.
For all these repetitive task, I can recommend using
Ant.
The way you describe it is not very common, and not at all practical; you deploy the class files, war, ear file, html files etc. but not the
Java source files. The only exception are the
JSP files; some people actually edit the deployed JSP's. Just look in the deployed folder of Tomcat, find the JSP, edit it and lookup the page again.
Hope this helps

== <br />Rgrds,<br />Eelco<br /> <br />SCJP, SCJD, SCBCD, SCWD, SCEA