The pair were arrested on Tuesday morning, 19 days after the blaze broke out at their home in Allenton, Derby.
Duwayne, 13, Jade, 10, John, nine, Jack, eight, Jessie, six, and five-year-old Jayden were all asleep upstairs in the property and died of smoke inhalation.
A man and a woman had to be escorted from the court by police and court officials after shouting out "scum" and "bastards" during the 10-minute hearing.
The Philpotts, who showed no emotion as they stood in the dock, were remanded into custody.
They will appear at Nottingham Crown Court tomorrow.
Last night a Crown Prosecution Service spokesman said: "The evidence was reviewed by a Crown Advocate from the CPS East Midlands Complex Casework Unit, who decided that there was sufficient evidence to charge and that it is in the public interest for a prosecution to take place.
"It is important to note that the defendants are entitled to a fair trial and nothing should be said or reported that would prejudice that right."
Assistant Chief Constable Steve Cotterill said: "Following the appeal yesterday a number of people have come forward with more information but I want to stress that the two charges this evening should not be seen as the end of the investigation.
"We are determined to get to the truth of what happened and still want people to speak to us to tell us what they know about this tragedy."
