George Brown, from Ballygawley Road, Aghadowey, pleaded not guilty to manslaughter when he was formally arraigned before Coleraine Crown Court.
He was released on continuing bail until his trial in February.
Mr Brown, 52, also denied a further 19 charges involving failures in health and safety legislation.
They include failure to protect non-employees, such as the two former prefects from Glengormley High School, failing to ensure those fitting gas appliances were qualified, and incorrectly fitting and failing to test that appliances were correctly connected.
Although no details were given to the court, sitting in Belfast’s Laganside courthouse, it is alleged the work was carried out across the north Antrim and County Londonderry coasts in the months ahead of the double tragedy.
This work not only involved the holiday home in which the teenagers were staying, but 14 other premises, including around a dozen homes, a restaurant and a caravan park.
Neil and Aaron had been on a break in the seaside town before getting their exam results.
The 18-year-old friends, from Newtownabbey in County Antrim, died on 3 August, 2010.
They were found by their parents, who went to Castlerock when they were unable to contact the young men.
It is estimated the trial will last between three to four weeks.