Where to call hook modifyImportRow? I'm using this Import plugin https://github.com/boboldehampsink/import.
 It has a hook called modifyImportRow, which would let me process single .csv rows with my custom logic.

In this case I have to process a Matrix field.

I'm not sure where and how to call hooks in general. In the plugin? In another plugin like businessLogic? Is there a specific file?
You'd do it from another plugin, just as if you were latching onto any of Craft's native hooks.

https://craftcms.com/docs/plugins/hooks-and-events

You can use the businessLogic plugin as a starting point or use https://pluginfactory.io to generate boilerplate plugin code.