Preference is called SEND ORDER FULFILLED CONFIRMATION EMAILS and is found under Setup > Accounting > Preferences > Accounting Preferences, in the Order Management, Fulfillment section.
If that is enabled then all you can do is customise the template with limited access to fields.
The fields are:
{1} is replaced with the customer name.
{2} is replaced with the order confirmation number.
{3} is replaced with the item list table.
{4} is replaced with the order tracking information.
{5} is replaced with a link to the Customer Center.
{6} is replaced with your company name.
{7} is replaced with the order tracking message and Customer Center link.
If you want more customisation, disable that preference and create a saved search that sends an email alert to the customer when it’s saved, or create an email template to use when a user send an email from the Fulfillment record. Either way you can construct a much more customised template referencing fields the way you’re used to, which one depends on whether you want it sent automatically or manually.