Bulk Order Fulfillment / Fulfillment Email Questions

I am trying to figure out the difference between these two options:

Setup>Accounting>Accounting Preferences>Order Management:

Send Order Fulfilled Confirmation Emails

and

Setup>Website>Setup Website>Email>Confirmation Emails to Send:

Order Fulfilled

Can someone explain to me the difference between the two?

I am trying to use Transactions>Sales>Fulfill Sales Orders to bulk fulfill shipments which works great except I want to email each customer their tracking information. Before I started using Mass Fulfillment, I'd go into each fulfillment and check the "Ship Notification Email Addresses" box. I couldn't find a way to have this box checked by default so I enabled the Setup>Website>Setup Website>Email>Confirmation Emails to Send: Order Fulfilled thinking that at least customers would get a generic email and could access tracking. That worked but then this new problem emerged when we receive/fulfill drop-ship PO's before we have tracking and/or before