NetSuite subsidiaries represent various subdivisions of your overall company. In FarApp, you'll want to set up each of your subsidiaries as their own account within their connectors. For example, if you have a "Domestic" and "International" subsidiary you wanted to use with your Shopify connection, then you'd want to have a "Domestic" and "International" account under that connector.
Once this is done, click on the connector in the navigation menu, then select the account for the subsidiary you wish to map. Click "Mappings", then "Orders", then "Order" at the top of the screen.
Select "Add Mapping" at the top of the screen, and select "Subsidiary" as the destination field. Click "Add Mapping". Next, click "Reload NetSuite Lists" on the bottom of the screen to be sure that you're using the most recent information. Last, in the dropdown to the right of "Fixed", select the subsidiary you wish to use. Then click "Save" to make the new mapping active.