The second day of the Long Island Rail Road’s “summer of hell” again went relatively smoothly, with MTA officials using lessons they learned on Day 1 to further ease the commutes of tens of thousands of impacted riders.

With newly implemented free bus transfers for commuters stepping off ferries in Manhattan, and subway turnstiles removed at Atlantic Terminal to streamline passenger flow, the Metropolitan Transportation Authority exhibited the promised flexibility in its plan to work around Amtrak’s summerlong track outages at Penn Station, used by 600,000 commuters daily.

More changes are on the way. After the second day of very light demand on express buses between eight Long Island locations and Manhattan, MTA Chairman Joseph Lhota said Tuesday that the service would be scaled back in the coming days.

“They’re just not being used,” Lhota said. “We provided our customers an abundance of choice. And based on two days, they’ve chosen to take the ferry out of Glen Cove and different ways to get into Brooklyn or into Queens and then take the subway . . . over the buses. And that’s fine.”

Lhota said the times the buses run and the number of locations where they operate will likely be reduced, but did not provide a timeline for when the changes would be made. There will be no changes Wednesday to the MTA’s plan, he said.

“It went as planned today,” Lhota said during the evening rush. “In fact, I think today went a little easier than yesterday overall.”

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As they were on Monday, Tuesday’s rush hours were uneventful for the most part, although four morning trains were delayed because of “equipment trouble.” Lhota said ridership at Penn Station was 10 percent to 11 percent less than usual.

Arriving at the concourse at the Farley Post Office building from Port Washington Tuesday morning, Kristen Karoff said commuting this week during the beginning of what Gov. Andrew M. Cuomo dubbed “the summer of hell” has been a breeze.

“So far it’s been good,” said Karoff, who works for a midtown Manhattan law firm. However, she added, “We haven’t hit the brunt of it yet.”

That sense of caution was shared Tuesday by other officials, including MTA Board member Mitchell Pally. He thanked riders for their patience, diligence and flexibility so far, and said it was imperative that they keep that up.

“We have a long way to go,” Pally, of Stony Brook, said Tuesday morning. “We can only hope that every day was like yesterday [Monday]. I wish we could guarantee that every day was like yesterday. But the likelihood that every day will be like yesterday is slim, because things happen.”

Some already have.

By many rider accounts, the scene at Hunterspoint Avenue station in Queens, which MTA officials have encouraged commuters to use instead of Penn Station, has been particularly chaotic. One standing-room-only train departing from the station just before the evening rush was just three cars long, according to one commuter.

Pally acknowledged that the aging station, which is handling about double its usual 2,900 daily riders, “was never built to be a major transfer station.”

Brooklyn’s Atlantic Terminal continued to be crowded but chaos-free Tuesday.

Commuters said trains arriving and departing from Atlantic, one of the transit centers designated by LIRR officials to pick up the slack during the Penn renewal project, had more passengers than usual. But those trains also generally ran on time, commuters said.

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Bill Conway, a construction administrator for an architectural firm in lower Manhattan, said he had to stand for much of his trip on the 6:37 a.m. train from Bellrose to Atlantic Terminal.

“It was crowded and it was hot,” Conway said, “but it was on time.”

Kristin Bennett of Westbury, an administrator at Borough of Manhattan Community College, said she usually took the LIRR to Penn but the diversion to Atlantic Terminal has been just a small speed bump in her daily commute.

“It was fine,” said Bennett, 31, after she got off the 7:08 a.m. train from Hicksville. “I was able to connect to my train in Jamaica easily and on time. It does add five or seven minutes to my commute.”

Norman Eriksen of Greenlawn, who takes the train almost every day to Atlantic, sounded bummed out that other commuters had learned about the LIRR’s second-busiest hub in New York City.

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“The one thing I have noticed is that everybody is finding out about Atlantic Terminal,” said Eriksen, who works near the terminal at the Brooklyn Public Library. “My train last night was crowded. Every seat was taken and there were people standing in the aisle.”

Eriksen said he likes Atlantic because it is a small station. “It is easy to get in and out,” Eriksen said. “That’s a big advantage.”

Eriksen said he did not have faith that the “summer of hell” won’t turn into the Autumn of Angst.

“I don’t expect they will finish this in two months,” he said. “It is the MTA. This will be going on into September.”

Sen. Todd Kaminsky (D-Long Beach), one of the leading voices in Albany for LIRR reform, took notice of the fragile state of Long Island’s transportation network this summer, as Penn — the busiest rail hub in the country — operates at significantly reduced capacity while Amtrak works to replace aging track components. Amtrak has said it aims to have Penn Station back at full capacity on the first rush hour after Labor Day.

“With three tracks out of service at Penn Station, and incentives for Long Island commuters to utilize crowded alternatives such as Hunterspoint Avenue, future disruptions will prove disastrous for an already burdened system,” Kaminsky said. “While there has been only good news so far, it would be premature to celebrate.”

To ease the burden on the LIRR, the MTA has supplemented train service with the express buses and ferries to Manhattan out of Glen Cove and Long Island City. However, as on Monday, there were relatively few takers for any of the new services Tuesday.

The 6:10 a.m. ferry from Glen Cove to Wall Street/Pier 11 left Tuesday with 38 commuters, while the 6:35 a.m. ferry to 34th Street departed with 41.

At the Long Island City ferry terminal Tuesday morning, MTA workers outnumbered passengers on some of the ferries, which carried as few as two people. Similarly, at the Valley Stream LIRR station and the Melville Park & Ride, some express buses scheduled to go to Manhattan left completely empty, except for their drivers.

Others did embrace the train alternatives, including David Dean, 43, of West Hempstead. Dean, a usual Penn commuter, took an LIRR train to Hunterspoint Avenue, and then hopped on a shuttle bus to a connecting ferry to get to his job as building service supervisor for the NYU Langone Medical Center.

“I am going to be a few minutes late, but I made the adjustment,” said Dean, who has experienced no major hiccups in his commutes so far this week. “All things considered . . . I think they’re doing their best to accommodate the riders. And, it’s working.”

In the afternoon, the massive yacht Tails of The Sea arrived at Long Island City from 34th Street in Manhattan with more than a half-dozen crew on board, but no passengers. The second ferry carried two passengers, Kevin Prestia, 44, and his wife, Keri Prestia, 39, of Roslyn.

The couple, heading home, was catching the 4:44 p.m. from LIRR’s Long Island City station.

“I’ve been enjoying the commute more than I normally do, actually. It’s relaxing to me,” said Kevin Prestia, an assistant professor of pathology at New York University. “Taking the ferry is just a great way to get to Manhattan.”