When it comes to inventory syncing, Trunk totals the quantities across all your Square locations and uses that to sync to your other sales channels. When another sales channel syncs to Square, it'll evenly distribute the quantities between all your locations.
For example, if your Square 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 Square 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.
If any of these behaviors are an issue, please reach out and we can definitely look into implementing another strategy for you!