Can someone confirm if I am playing this right:

You shuffle green and red epic cards then stack green's on top of red's, right? After first upkeep you draw the first green one and resolve it.

It seems that the red deck comes into play very rarely. And what about sinister plot cards? They also come very rarely into play. Am I wrong on this? Can someone maybe give me an example? Played just once with this.

You are correct. Two of the three "Sinister Plot" triggers are in the red deck, and they come out very rarely. That's why I've been employing a house-rule that makes reds more common when you have fewer seals and when battle goes on longer.

Cardinal Nicodemus said:

You are playing it correctly.

The red deck does come into play rarely, yes. The Sinister Plot cards, on the other hand, come into play all the time. There is one green "draw a Sinister Plot" card, which can of course wind up anywhere from the very first card you draw to the eighth. Sometimes the fight is finished before we reach that card, but much more often we draw a Sinister Plot card before the final fight is done.

Thanks for all the help. I think that I will somewhat house rule the epic deck so that red cards come into play more often. Would mixing both decks together be a good idea?

Here's what I've been doing:

Set aside the red "End of Everything" and green "Sinister Plot."

Shuffle reds and put "EoE" on bottom. Put "Sinister Plot" on top.

Shuffle the remaining greens and (randomly) put one on top of the stack for each seal on the board. Remove the rest from play.

When a round starts, instead of taking the card on top, roll a die and take that number card from the top. If you roll higher than there are cards left, you automatically get "End of Everything."