When it comes to inventory syncing, Trunk totals the quantities across all your Shopify locations and uses that to sync to your other sales channels. When another sales channel syncs to Shopify, it'll do its best to distribute the quantities between all your locations.
For example, if your Shopify locations have quantities of 10 and 5, that would bring the total quantity to 15 which Trunk syncs to your other sales channels. If you were to sell a quantity of 2 on another sales channel, then Trunk would sync to your Shopify locations: 8 and 5. Essentially, Trunk will subtract from the location with the most surplus. Trunk also supports subtracting/adding inventory from a default location if that's your preference.
Trunk also supports excluding locations but you'll need to contact us in order to have us configure this for you.