Have you seen this thread?:
With mixintos you can add new content or modify existing content.
Overrides replace entire files (either qb models, json files, lua files, etc). It can be dangerous to override things other than models, so mixintos are always preferred (and there’s a way to remove content with mixintos too).
There are many features in Stonehearth based on an index (for example, recipes for the crafters). You can add your own lines to that index via a mixinto. To reference your new items, you add your own aliases in your manifest and then use them in your mixintos.