This sounds like The Spell of the Sorcerer's Skull by John Bellairs.
Professor Childermass has disappeared. And Johnny Dixon can find few clues: a haunted dollhouse and a lighted, menacing jack-o'-lantern. The dollhouse is a miniature replica of a room in the Childermass family home -- the same room where the professor's granduncle Lucius died in a very bizarre way. When Johnny takes a tiny skull from the dollhouse, demonic forces are unleashed -- forces that capture the professor and lead Johnny and his friends Fergie and Father Higgins on a harrowing chase to the deserted islands of Maine. There, waiting for them, is something far more terrifying than they could have imagined.
The skull is that of a warlock named Warren Windrow who was hanged for the attempted murder of Professor Childermass's ancestor Lucius. After the execution, Lucius bribed officials to
turn the dead man's skull over to him.
"Ah, but good old Lucius knew nothing of this, so he put Windrow's skull in a hatbox and took it back with him. He went to live at our old place in Vermont, and the hatbox wound up on a shelf in his bedroom closet."
After Lucius died mysteriously...
"What they found was a teeny-tiny skull, the same one that wound up on the shelf by the fireplace in the dollhouse room that some of us here have seen."
I don't see any mention of a character named Mortimer or a prayer banner, but a crucifix and part of a Catholic hymn are integral to the climax.