Iron Vault has support for Settlements by using the related Oracle Entity, which can be rolled either through the Sidebar or through the Generate an entity command. You'll be given the option to save the results into a new file, which will include a Markdown table with all the roll results. Rolling this oracle group will also record the results in your journal.
Besides this, there is no additional support specific to locations and settlements. You are free to organize these entities however you want, including having multiple settlements in a single file (although we recommend doing 1-entity, 1-file as a general rule).
For mapping, you can use anything you want! One idea might be to generate maps with something like Procgen Arcana, StationArchitect or DungeonDraft then use this guide on creating an interactive map to make it all very pretty and linkable.