Hello Joseph and welcome to the AmiKit Support forum.
The Workbench has changed since Amiga 500. Not radically but many many things were enhanced, etc. In addition the AmiKit Workbench is even more enhanced. Actually AmiKit uses a Workbench replacement called Directory Opus Magellan which behaves and looks similar but is much more powerful. Once you get used to it you realize you gained maximum control over your files as the file management is much more sophisticated than in default WinXP.
There's no extra comprehensive manual on how to use AmiKit. Simply go and try, there's nothing you can do wrong. In the worst case simply re-install AmiKit and that's it. You might want to check the (old) tutorial videos
of AmiKit to get a brief idea how to work with it.
I am not sure where to start, what to explain first. At the beginning look at the following sites that describe several areas regarding Amiga and its emulation on Windows machines:http://www.tweakguides.com/Amiga_1.htmlhttp://ale.emuunlim.com/guides/guides.shtmlhttp://www.pcguru.plus.com/uae_faq.html
You might want to visit general Amiga forums where many people are ready to help you:http://www.amiga.org/http://www.amigaworld.net/http://www.amigans.net/
Cloanto's Amiga Forever page is also a very good source of information:http://www.amigaforever.com/
The history of Amiga is described here:http://www.amigahistory.co.uk/amigaos30.html