its actually a lot easier to do it by hand. the auto gen usually screws up quite badly unless your layout is very simple. you end up spending more time doing damage control than you would have by doing it manually IMO
This. Only auto generate it if you have, like me, a giant 1100 cell exterior worldspace to navmesh. At that point you'll still have to do a lot of correcting, and will likely have to go over every single cell to check it, but it wont take as long as doing it by hand. However, for just about every interior and small exterior change, do it by hand.