If you use Spiritomb's "Ghostly Cries" attack, can you put more damage counters onto a Pokemon than it would take to Knock It out?
Yes, you can. You place all the damage counters for Ghostly Cries first, then resolve any Knock Outs from the attack.
Source: Chilling Reign FAQ; TPCi Rules Team (2021-06-17)
For Spiritomb's "Ghostly Cries" attack, do you put any Pokemon Knocked Out by the attack into the discard pile before or after shuffling all the Pokemon in their discard pile back into their deck?
After. Shuffle the discarded Pokemon into the deck first, then resolve any Knock Outs from the attack.
Source: Chilling Reign FAQ; TPCi Rules Team (2021-06-17)