I use gliffy.com and a normal wiki page
it is quite hard to write a multidimensional explorative documentation I think the best representation are multidimensional graphs :) so you can go through all levels and relations between the systems.
personally for documentation I don't care about user stories ... they are 1 paradigm to formulate a given scenario and the wanted output. :)
but in theory you can link them as well.
That's how I do it :)