PDF viewer that makes reference checking easy
This is not a split screen solution, but an easy keyboard shortcut to switch between end and current view.

Preview

In Preview you can jump back and forward in your "viewing history" with cmd+[ and cmd+]. After switching to the references at the end with end (or fn+→), you can jump back at the exact same view you were before with cmd+[.

Also remember the page number that is seen in Title bar of Preview and use alt + cmd + G to navigate. 

Acrobat Reader

In Acrobat you can do the same and navigate through the page history with cmd+← and cmd+→.