> I understand there
are 2 indexes automatically generated, but wich one is the "top index"?
OK. After some testing I think I know which is the difference between both
options:

option -I (make an index) creates a file called "index.html" inside the folder
written in path option (-O). E.g., in my tree it would be created inside
"mirror1". Note that this is a default option, so this index will be created
on every mirror, unless you use -I0.

option -%i (make a top index) creates a file also called "index.html", but now
it's located inside the "golbal/general/top" folder containing all of your
mirrors. Everytime it is recreated, the robot looks for any new, modified or
deleted mirror and updates the file acordingly. E.g., in my tree it would be
created inside "websites", linking to "index.html" inside "mirror1". Note:
this is a per user option, so if you want a "general index" you have to add
-%i in your list of options