Once you've created new templates you can select which ones to use as default against your company or "channel brand". Go to Settings > Company > Company information. Click to edit your channel brand and select the templates tab.
When you have multiple channel brands you can select different templates, or use the same ones! Remember to also upload your logo so this will also pull into the templates!
When you have different shipping methods you can select different goods-out notes templates per shipping method at Settings > Shipping > Shipping methods. Click the edit your shipping method and select the templates tab.
Until you select which templates you want to use as defaults Brightpearl will always select these templates (with their ID numbers):