The pair appeared separately before Judge Carrie Wainwright.
Waipuka appeared first, wearing a yellow T-shirt and sporting a rats-tail hairdo.
The short-statured 17-year-old, wearing a blue hood jacket, stood barely above the glass partition of the dock.
From the public gallery, family members of the 17-year-old called out "mama loves you''and "take care boy''.
Speaking outside court, Detective Senior Sergeant Scott Miller said he hoped this initial resolution brought some comfort to Cottrell's family and colleagues.
He said the investigation was not anywhere near the end.
"In fact, it's just beginning.''
Sombre ceremony
Family and colleagues of Mr Cottrell gathered this morning for a sombre blessing of the site where he was fatally beaten.
Cottrell's sister and brother-in-law, Sue and Heath Hollows, and about 20 colleagues gathered this morning on the stretch of Boulcott St in central Wellington where he was attacked.
Minister Andrew Bollen of the Central Baptist Church, right next door to where the attack happened, led those gathered in the Lord's Prayer.
The site was blessed with holy water before tearful colleagues took turns to lay flowers and fern fronds on the footpath and against a wooden fence.
A tearful Don Rood, head of news at Radio New Zealand, said the blessing would help to bring reassurance to those affected by the "senseless'' attack.
"We will miss him,'' he said.
Another colleague paid tribute to Cottrell's good nature and described the attack as "all sorts of horrible''.
Mr Hollows said he was no good with words but thanked those who were gathered.
A memorial service for Cottrell will be held at St Andrews church on the Terrace at 1pm on Friday followed by a private cremation.
The family has requested no media coverage of the service.
Earlier today, Ms Hollows paid tribute to her brother on behalf of the family, saying they were "deeply shocked and saddened that this kind and gentle man would be taken from us in such a brutal way''.
"On behalf of our family, we want to thank all Phil's friends and colleagues who have supported us at the hospital and in all of these horrible days following. We know they share in our grief.
"We were comforted to know that someone loving was always by Phil's side, even before we could get to Wellington to be with him.''
Ms Hollows said the family was deeply grateful to intensive care staff at Wellington Hospital and to the police investigating the attack.
"We understand that many messages of condolences have been sent to Radio New Zealand from all over the country and internationally. To all those people who have been thinking of Phil, we thank you.''
In a death notice this morning, the family said they were grateful above all to the taxi driver who first found Cottrell and called emergency services.
"Words cannot express the gift that you gave to both ourselves and Phillip ... the gift of farewell.''
