Karen Matthews pleaded not guilty to the charges as well as an earlier one of perverting the course of justice over nine-year-old Shannon's disappearance in February and March this year.
Michael Donovan, 40, the uncle of Matthews's former partner Craig Meehan, also denied the same three charges at Leeds Crown Court yesterday.
Matthews, 32, of Moorside Road, Dewsbury Moor, and Donovan, of Lidgate Gardens, Batley Carr, were brought into the dock together.
Throughout the 45-minute hearing the two sat about a foot apart and did not look at each other once.
Heavily made-up Matthews was dressed in a beige jacket, white blouse and dark trousers. She appeared to have put on weight while on remand and her hair was longer than when last seen in public.
She spoke only to confirm her details and to enter her pleas. Otherwise, she listened intently to what was being said in court and stared straight ahead with a grim look on her face.
Donovan was dressed in a navy blue sweatshirt and grey jogging bottoms. He appeared pale and drawn, and had red bags under his eyes. Unlike Matthews, he at times appeared distracted, his gaze flitting round the court.
Matthews is to be represented by barristers Richard Butters and Frances Oldham, while Donovan's barrister is Ahmed Nadim.
Simon Kealey and Julian Goose are to prosecute the case.
Matthews and Donovan are expected to return to court on October 24 for a case management hearing. Following that they will be tried from Tuesday, November 11, a hearing which is expected to last for three weeks.
Shannon, a Westmoor Junior School pupil, vanished after going on a swimming trip on February 19.
Police mounted a massive investigation involving hundreds of officers and a team of 60 detectives to try to find her.
She was eventually found in a drawer of a bed 24 days later.