They should print out the eticket document for the second flights (Eagle) and have that when they check in for Emirates.
When they leave immigrations/customs at the lower level in D there will be a belt for recheck- if they havent bee able to check through, there will be check in counters just beyond the belt with agents to check them in. All in the same large area just outside of customs, so they dont need to go anywhere else.
The security check upstairs can get long (esp without precheck) so some folks will travel to the next entry. It is a bit of a walk. I mention this just in case.