South-bound motorists should choose their lane before the Harbour Bridge.
Town said new overhead signs, starting north of the Harbour Bridge, would guide drivers into the correct lane.
"The risk is people weaving across lanes to get ahead. If they make the wrong choice they will not be able to change lanes on the flyover because of the central barrier."
The two lanes to the left of the flyover's central barrier are for those going to the central business district, the port or Northwestern Motorway. The two on the right are for those travelling south.
A concrete barrier between the left lanes and the right lanes will stop drivers moving between them.
One of the two existing exit lanes to Fanshawe St will become a bus lane, but the exit will branch out to four vehicle lanes towards its intersection with Beaumont St.
Reduced summer traffic would help as motorists got used to the change.
Auckland Mayor Len Brown urged motorists to cut their speed and choose their lane early.
"The key to making this work best is patience," he said.
Browns Bay resident Max Gibson expects teething problems on his daily commute to Pakuranga. He had already witnessed two nail-biting, last-minute lane changes while the roadworks were under way. But he welcomed the changes.
Fellow commuter Wesley Hill, of Forrest Hill, said the flyover would stop selfish drivers changing into the correct lane at the last minute.
The Victoria Park Tunnel, which is part of the same project and opened in November, has confused some north-bound motorists, who slow down at the tunnel entrance and cause congestion.
More than 150,000 vehicles use the route each day.
You're in my lane!
I'm new to Auckland but the menacing sight of a car travelling towards me, the wrong way down State Highway 18's Hobsonville extension, was one for the memoirs.
It was New Year's Day and there was little traffic. I was passing a slower vehicle when over a crest, a car appeared. It was
going the wrong way.
I just wrenched the wheel left, and other cars behind me did the same.
Inspector Shannan Gray, in charge of policing Auckland motorways, said the elderly male driver went the wrong way after a u-turn near Greenhithe Bridge.
Eighteen months ago, unlicensed driver Ewen Donaldson, 86, and his passenger died in a six-vehicle pile-up when he drove the wrong way down the Northwestern Motorway.
Two years earlier, Odette Thompson, 33, died driving the wrong way down the same motorway.
