I have built my IEAK Browser Package with the IE Pre-Reqs, but after IE 11 installs the machine needs to reboot and then after reboot I need additional Updates installed for Enterprise Mode to work... What would be the best approach in deploying this in SCCM? 

You've got multiple options:

1. The application model and use dependencies to connect the updates with IE;
2. The old-school packages and use the run another program first to connect the updates with IE;
3. A task sequence and add IE and the updates in the required order.

Personally, I think the third option gives you the most control over the action. Also, it will probably provide the best information to the end-user.

Yeah I agree working on Option 3 now...  Thanks!