I use org-mode uber outliner of Emacs editor/environment. For organizing everything, not just musical projects. It’s kinda geeky tool but it has, amongst thousands of other features, very nice table editing capabilities. It allows me to quickly note I/O routing of the gear into simple matrix tables. I gues any spreadsheet editor would do it too.

For visual routing plannig I use yEd, free scheme drawing tool with a lot of cool features.