In Mystara, IMO the most appropriate location could be north eastern Davania. It also suggest to unify Ghostwalk deities with Greyhawk ones. The book also has suggestions for Greyhawk: replace the Yeomanry and the Hold of the Sea Princes, or the Amedio Jungle, or the Lendore Isles or the eastern part of the old Great Kingdom. It also suggest to unify Ghostwalk's deities with some FR ones, or even place Ghostwalk in an undeveloped part of Maztica and keep the same deities (Ghostwalk's common culture however seems a bit too european for Maztica.) The latter could be the best choice, having yuan-ti nearby.
In the Forgotten Realms the book suggest to place Manifest in Lantan, Moonshae or Tashalar.
It however suggest to place it in a remote area of your campaign world to explain while rules about life and death are different around the city of Manifest. of Ghostwalk explicitly says it is intended as a stand-alone setting. Probably an error, there is nothing explicitly tying it to the FR, the assumptions about life after death are quite different. However a few days ago I saw it was listed in the Forgotten Realms wikia among 3ed FR products. I have Ghostwalk but I always thought to use it in its own world, even if it's not very developed beyond the surrounding region.
