Iron Vault has support for NPCs by using various Oracle Groups, which can be rolled either through the Sidebar or through the Ask the Oracle command. For example, rolling the Character Oracles Oracle Group by pressing the dice icon in the sidebar, or invoking the Generate an entity command will pop up a window where you can do a batch roll of all oracles in that group, or only the "first look" oracles. You'll also 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 NPCs. 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).
You are free to manage the representation of Connections however you want, but one recommended way is to first use the Create a progress track command to create a new Connection progress track, then embed that track in your NPC's file using ![[Connection to My NPC|iv-embed]], which will inline an interactive version of the progress track right in your NPC file. You can also add metadata to your frontmatter, such as connection: true and bond: true.