After you've created e-mail templates or packing slips specific to each of your stores, it's easy to assign the e-mail template to the store to which they belong.
*Please note that you must be on a Silver or above plan to customize your packing slip, though the instructions below will still work for your custom e-mail templates.
Head to your Account Settings (the wrench icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left.
You'll see a list all of the stores that you have setup within ShipStation. Find the store that needs an e-mail template or packing slip template assignment, and click Edit.
Click the Notifications sub-tab and you'll see drop-down options that control the default e-mail notification templates for your store, and click the Packing Slips sub-tab to see the drop down option that controls the default packing slip template for your store.
Choose the ones you wish to use with your store, fill out any of the optional settings, and when you've finished, click the Save Changes button at the bottom.
Please note that you can't use ShipStation to send confirmation emails to encrypted Amazon email addresses (those ending in "marketplace.amazon.com") or for your Rakuten/Buy.com shipments. These companies don't allow us to send confirmation emails for their orders, so you would have to edit those e-mail confirmation settings in your respective marketplace accounts.
*You can still change these options on an order-by-order basis, should an order call for a specific e-mail or packing slip.