Bukkit's Weird File Paths

So I am running a server using Bukkit. When I first tried to use Bukkit I couldnt get it to work. So then I tried hey0. That didnt work as well. So as I was fiddling with things I got it in my head to do a search of my entire Hard drive for the server.properties file. It found one in the folder where the server software was (Where it should be) and it found one generated by the software in my Windows/sys64 folder. I then went back to Bukkit and was able to set the server up. I decided to just let it go since it worked and thats all I wanted. Well just now I tried to install a plugin...which according to the plugin installation faq it should have auto loaded and I would have been done with it.

Well...it didnt work the way it should have. Now I havent done another search (Since it would be futile as I have many games with many plugin folders.) but I wonder if this is a Bukkit glitch or some random bug in my Windows 7 installation.

Help would be appreciated. I'm ready to edit files to redo file paths if need be. Also a list of self generated files that Bukkit creates would be nice...as after I fix this problem I will need to go through my system and clear those out. As I dislike clutter.

 

Is your plugin in the plugin folder? also is your plugin compressed in a rar? Or is it for sure the .jar file in your plugin folder? Please im not trying to sound condescending Im just trying to cover the basics to narrow it down.