To created merged board:

Use eagle-brd-merge python script (https://github.com/p12tic/eagle-brd-merge)
Command:
merge.py merge.brd Mother\ v1.0\ -\ panel.brd Child\ v1.0\ -\ panel1.brd --offx .83375mm --offy 50mm

moves child board up 50mm and right a small amount to line up w/ main board cutouts.