This is what Cascade Games told me in a follow-up email:
The entry fee is for the main event, which is an individual flight. That is what most people do, though we have plenty of popular side events as well.
The $40 for 2-Headed Giant is per team ($20 per player). Both players receive a pre-release foil, while supplies last.
Many people do play in more than one event at a time. Sometimes we sell out of Open Dueling product before 4pm on Saturday, so we have another suggestion.
You may want to consider signing up for the event that you want to play in (sounds like 2-Headed Giant), and while registration is still going, sign up for Open Dueling as well. You can find people to play Open Dueling matches against, casually, throughout the day (before your tournament, in between matches, and after your tournament), but focus on the 2-Headed Giant event.
This way, even if you are really busy with the 2-Headed Giant tournament, you will still have the Open Dueling product (and score card), and can find people to play later in the afternoon when you are done with 2HG.