The pilot scheme is aimed at making the lay-bys more conspicuous to motorists who need to stop urgently when the hard shoulder has been converted into a running lane for traffic.
Highways England launched the trial by giving one refuge area on the M3 in Surrey an orange road surface and better signage featuring the SOS acronym.
It hopes the redesign will improve the lay-by's visibility and encourage drivers to only use it in critical situations such as a breakdown.
The measures will be replicated elsewhere unless they do not have the desired effect.
The change is part of an ongoing review into the design and spacing of refuge areas on smart motorways that is due to be published in the autumn.
A recent RAC poll of more than 2,000 drivers found most (52%) are unaware of what the emergency lay-bys are, and almost two-thirds (64%) do not know what they would do if they stopped in one.
Highways England chief executive Jim O'Sullivan said: "We know that smart motorways are safe. But we also recognise that drivers need to have confidence when using them and be clear about where they can stop in an emergency.
"That is why we are trialling these highly visible new-style emergency areas. The bright orange colouring will make them as easy as possible to spot and should also discourage drivers from using them in non-emergency situations."
The Department for Transport has been keen to press ahead with smart motorway projects in a bid to increase capacity without widening roads.
Transport Secretary Chris Grayling said: "Smart motorways are adding extra lanes to our busiest motorways and - as recent evidence shows - reducing the rate of crashes.
"We are making emergency refuge areas more visible to ensure motorists in trouble can easily identify where to stop safely."
Concerns have been raised that the maximum distance between lay-bys of 1.6 miles is insufficient to avoid broken down vehicles being forced to stop in live running lines, putting them at risk of being hit from behind.
Some motorists have described the areas as "death zones" and "desperate unreachable havens", according to the AA.
The motoring firm's president Edmund King said: "We were consulted on the redesign and supported the steps to make the emergency lay-bys more obvious. This is a step in the right direction.
"However, approximately one-third of drivers don't use the inside lane for fear of broken down vehicles ahead, so what we really need is more emergency lay-bys and not just more paint."
RAC road safety spokesman Pete Williams predicted the trial will "significantly improve visibility and make it easier for drivers to find a place of relative safety".
But he added: "Safety would be further enhanced by additional emergency refuge areas to reduce the likelihood of vehicles being stranded in live lanes."