I'm brand new to JBoss myself, although I've been using Java for a couple of years now. I'll try my best to answer your questions and hopefully I won't mess it up too badly.
1) I haven't actually done it yet (that's tomorrow's exercise) but, like you said, the instructions say that Tomcat files should be deployed to the deploy folder for the server configuration you are using.
2) As for why there are four deploy folders, there is a deploy folder for each main server configuration (all, default, minimal and standard ... which refer to what features / MBeans start up automatically when you start JBoss). If you're not using the "-c" switch when you are starting JBoss, you're probably using the default server configuration.
3) Most of the files are duplicates because they are all subsets of what is included in the "all" configuration. See section 2.1.2 of the "Getting Started" guide for descriptions of these.
4) I don't know yet, but if I figure it out before a more experienced user posts the answer here, I'll post another reply with the answer.
1. Where do I place the jsp files exactly for them to work in JBOSS
You should study the structure of web application archives (WAR). You can place your jsp files in a war file and put it in the deploy directory of the "default" configuration.
2. The pdf file for JBOSS getting started talks about placing my code into the deploy folder. well there are 4 deploy folders [server\all,server\default,server\minimal and server\standard] so which folder am I to place the files into?
These are various configurations of JBoss that you would use dependent on what features you want from JBoss. For your basic needs, go with "default" configuration.
3. Why is it that most of the files in these 3 areas are duplicates?
As I said these are different configurations of Jboss. Look at them as three different types of Jboss servers with different types of services. Ofcourse you will have common services like web container, JCA etc? Correct?
If you want to drop simply deploy a jsp page or html file, you'll have to read this as what you are trying to do is deploy an application in 'exploded' form.