Quote Originally Posted by Great Dragon View Post
Should I put each Skull in a separate room?
Each with only 25 Flying Skulls.
I was going to say something but...

Quote Originally Posted by Great Dragon View Post
The party defeated the Skullyard!!!
By the skin of their teeth.
Though I have something to say about...

Quote Originally Posted by Great Dragon View Post
One Skull = easy Encounter.
Two Skulls = moderate Encounter
Three Skulls = hard Encounter
Four Skulls = deadly Encounter.

Is this correct?
According the CR system, an encounter with a challenge rating of 5 is a moderate encounter for a lv 5 party, and a CR of 10 would be a deadly encounter for a lv 5 party.

According to the exp system though the fact that there is less of them than you (In the case you did have them all in separate rooms, or maybe split them into groups), the encounter difficulty would actually decrease due to action economy. The exp system is far more accurate, but it can be difficult to remember all the rules for calculating difficulty with that.

I congratulate your party on surviving that, they defeated a total CR of 20 (twice a deadly encounter), and I think that if the skulls hiding and maybe redirect abilities were factored in, they would almost deserve a CR of 6. If you did indeed have the skulls all in the same room then its amazing the players survived.