I use yEd for drawing this kind of thing. It allows me to make a horribble mess of boxes and arrows, then auto-cleans it up with a few clicks in the menu.
It requires making sone compromises, however: Box inside box does not always end well. It is a worthy tradeoff for me, as I can document things much faster, and you get a feel about what will or wont work after a few tries.
Is yEd free to use? The underlying yWorks SDK seems to cost 5 figures for one developer working on one web site. It must be very capable to have customers for ~20 years.
Their page states it is freely available. I cant seem to find the license on their website, unfortunately. I believe it started out as a demo for their paid library, but turned out to be a good standalone application.
It requires making sone compromises, however: Box inside box does not always end well. It is a worthy tradeoff for me, as I can document things much faster, and you get a feel about what will or wont work after a few tries.