Does End of Days affect cards underneath another card (e.g. The Dreamer's defeated Projections)?
I tested this in the app version of the game. 


The cards under The Dreamer they are destroyed
The cards are put back under The Dreamer, per its effect
If some other card would interact (Like Savage Mana), that takes precedence and would be destroyed afterwards


Also don't forget that it's the players that choose which effect resolve first and which cards are destroyed first.