Murder suspect Michael Thomas Rafferty, 28, is shown in an undated photo.
McClintic originally told police that her then-boyfriend Rafferty killed Tori, but on the stand at his trial, she said she bashed the little girl to death.
In his charge to the jurors before they decide Rafferty's fate, Heeney said the fact McClintic, 21, pleaded guilty to Tori's murder and is serving a life sentence shouldn't be considered in deciding whether Rafferty is guilty.
Rafferty, 31, is accused of abducting, raping and murdering Tori.
Her battered body was found under a rock pile near Mount Forest, Ont., on July 19, 2009, 103 days after she was abducted outside her school in Woodstock, Ont.
Heeney told the jurors they will have to decide whether Rafferty's various "coverup" activities after Tori's disappearance and murder are evidence of guilt or if there was some other explanation.
The judge explained that a kidnapping charge means confining or moving someone "through force or fraud" and that they will have to decide whether the circumstances of Tori's disappearance qualify.
He also warned the jurors not to judge Rafferty's overall character or guilt or innocence based on the number of women he met via online dating sites.
The address to the jury is expected to be completed Thursday. The jury will then deliberate.
Watch our live chat below for a detailed breakdown of the judge's instructions.