Stuart stood behind Colin during the hearing and the two did not appear to interact in any way.
They defentants are both charged with two felony counts of child abuse and corporal injury on a child. They face up to seven years and four months in prison if convicted.
The children are currently in protective custody.
Police found Stuart's 5-year-old and 2-year-old sons badly bruised, malnourished and dehydrated on Wednesday after a welfare check on the kids. Stuart's landlord reportedly called police, saying he seldom saw the kids, and when he did, they appeared battered.
Police found the younger boy with severe bruising to his forehead and cheek, and his lips were so dry they had cracked and bled, said Cpl. Anthony Bertagna, the Santa Ana police spokesman. The 5-year-old had swollen arms and was extremely dehydrated, and both boys had bruises and knots on their heads, Bertagna said.
Police said Stuart confessed to tying the boys to their beds using shoelaces, Ace bandages and even chains.
Stuart allegedly told police the boys ran around their rented room, and she couldn't sleep. She also allegedly told police she had to discipline the 2-year-old because he wouldn't respond to potty training.
According to police, the two exchanged text messages in which Colin allegedly instructed Stuart on disciplining the children. It allegedly included depriving them of food and water.
Colin's involvement opens a new facet of the investigation. He was employed as a behavioral technician at Durfee Elementary School in Pico Rivera.
According to a district official, he helped with special-needs students, but did not discipline them. He was a probationary employee whose term was over in June after four months of work.
Police are trying to determine if he ever abused anyone at the school.
Police are also looking into Colin's home life. He did not live with Stuart, nor was he the father of the children. He lived with his wife and two children, who also may have been targets of child abuse. Police said Colin's wife only learned he was having an affair with Stuart on Friday when she spoke with detectives following his arrest.
Anyone with information about the alleged abuse is urged to call the Santa Ana Police Department at (714) 245-8400.