Holly and her best friend Jessica Chapman disappeared on 4 August.
Their bodies were found in neighbouring Suffolk on 17 August.
In an interview with the Cambridge Evening News Holly's father Kevin said the family was struggling "step by small step" to reach some kind of normality.
He said the days since the girls' deaths had been very dark for both families.
All of them knew that more difficult times lay ahead.
"As a family we are now trying to be as positive as we can be and creating an environment for Oliver (Holly's 12-year-old brother) which is conducive to his progress," said Mr Wells.
He and his wife Nicola have returned part-time to their jobs.
"We are just trying to keep taking those small steps towards a sense of normality.
"Having said that, over the last few days myself and Nicola have been very low and tearful again.
Nationwide response
"We've just been feeling so desperate at our loss of Holly.
"It's the small things which are the catalyst for our emotions.
"Little things which you notice or miss about Holly just trigger you off. "It's still very difficult to accept."
He said they, and Leslie and Sharon Chapman, had been taken aback by the nationwide response to the families' ordeal.
"It touched a chord in the nation's hearts because people could see that here were two beautiful young girls from loving families who were doing nothing wrong," he said.
"I think people just felt that is could so easily have been their daughters."
A trust fund set up for the families has now topped £25,000.
The fund was set up by two Soham businesswomen who are friends of the families.
Murder charge
Donations to the Holly and Jessica Appeal Fund can be made to any branch of the Cambridge Building Society.
Police investigating the girls' deaths have asked journalists to hand over film footage and notebooks if they contain evidence which could be valuable to the inquiry.
Ian Huntley, 28, from Soham, has been charged with murdering the girls and conspiring to pervert the course of justice.
Maxine Carr, 25, has been charged with perverting the course of justice.