Those directories are in /usr/src and they contain two sets of headers. You accessed them in Gnome by going Places > Computer > Filesystem > /usr/src or by accessing the "Computer" icon on your desktop. (See why we prefer to use the commandline?)
The first one is pretty much the vanilla kernel headers. -generic has the modifications for the ubuntu generic kernel (IIRC - it's been a while), you'll see it's mostly links to the other one. You can learn a lot by comparing these two.
Which is the "main" one depends on what you want to do.