How do I edit preferences with the new company settings? I need to change my default email that goes out with invoices.

Default for sending out email is always the same* which you cannot change it. What you can change is reply-to email address of your own for customers, different than regular company email address.

*default email address from Intuit[donotreply@intuit.com]

From the home page screen > company gear (upper right corner) > settings > company > contact info > add customer email (this is where you add email different from the company email address).