I’ve placed 2 plugins in different directories (according to their docs instructions).
One is in C:\Documents and Settings\Alex.AUTOINSTALL.001\Application Data\.emacs.d
(the plugin is yasnippet-0.6.1c).
I placed the second in D:\Program Files\emacs-23.1\site-lisp (the plugin is color-theme).
I think its a bit confusing to place plugins in different directories. It is possible to place them in only one directory? or because of the ‘nature’ of those plugins they must be placed in those separated directories?
You may put your elisp files wherever it’s convenient for you, as long as the directories you use for this purpose are on your load-path. For example, I have this line in my ~/.emacs file:
And most of my extra elisp resides there. (I’ve also got separate directories for larger apps.)
On Windows, you’ll be putting something similar in your _emacs file.