Are we supposed to add the additional libraries in the 'Libraries' folder will there be a special folder for these libraries ?
In agraham's B4AndroidHelp program there is a button 'Addnl.' which points to the same folder.
If I remember well, I read somewhere that there would be two folders.
Yes, there are two library folders. The implicit official libraries folder under Basic4android and one specified in Tools -> Configure Paths as "Additional libraries".
The reason there are two is to avoid having to copy additional non-official libraries to the Libraries folder under Basic4android in Program Files as copying there is subject to Vista/Windows 7 security management.
The contents of both libraries are shown in the IDE Libraries tab and there is no difference in use between them.
Note that the optional "additional libraries" folder is scanned first, so if the same library is located in both folders, the one from the additional libraries will be loaded (so there is no need to delete any of the original libraries if an official library is updated).