How do large sites manage and keep track of their development cycle ?

I am having to take on and debug a medium sized site which I did not build myself. The code is quite complex with a lot of self referencing code, conditionals and variable variables and a nest of functions.  Taking on other people's code is always 10x harder to understand that your own. 

In order to bring clarity to this rats nest I want to document the code so that if I have to back to it in 6 months I won't have to relearn it all over again.

So, other than pen and paper, standard flow charts are there prescribed methodologies for documenting sites ? How do the big boys do it ?

Thanks Vincej