There's no way to set one of your sales channels as "master" but there's also no need to! This is because Trunk syncs by timestamps and can track where and when a change was made and reconcile based off that. That means you can simply adjust the stock level on one of your sales channels (e.g. within your Shopify admin) and Trunk will automatically sync that to your other sales channels.
However, it's important to know that Trunk treats its own stock levels as the source of truth when it comes to connecting new sales channels. So if a SKU already exists within Trunk's inventory, the stock level there will initially be synced to any newly linked listings.