Yamaha dominated the season's first two grands prix with Maverick Vinales, but Marquez won from pole in America and moved up to third in the championship, 18 points off new leader Valentino Rossi.
Honda ran first and second for most of the race with Dani Pedrosa and Marquez, while Vinales had an early crash from fourth, and though his pace faded Pedrosa was still able to finish third behind Rossi.
The Japanese marque will test at Le Mans next Tuesday with Marquez and Pedrosa, who will both be using the second day of their five-day allocation for the season.
All five of MotoGP's other manufacturers will also be present at the French track, with Aprilia also opting to hold a private two-day test this week at Mugello.
Marquez, who dislocated his shoulder at Jerez in February during his first private test day of the year, believes the Le Mans test will be crucial for improving the RC213V to be able to take on Yamaha.
"It's important [to win] because we are third again in the championship," said Marquez, who had crashed when leading the previous race in Argentina. "Before the race I was eighth, and I said 'OK, we need to start coming back.'
"Still I don't feel perfect with the bike, we are missing something. Now we have an important test at Le Mans and an important race at Jerez.
"We need to understand [the problem], because if we understand it there and fix this problem, we can fight strongly for the championship."
Marquez was unsure where Honda's improvement relative to Yamaha had come from at Austin and said he had not been comfortable with the bike even on the way to victory.
"I was playing a lot with the set-up, trying to find stability and have more confidence," he said. "For some reason we didn't find it, then I was looking to tyre life because the front tyre I was destroying a lot.
"On Friday with just 12 laps my front tyre was destroyed and impossible to ride fast. Then on Saturday we did a great pace, but we don't know if it was the temperature.
"[In the race] everyone suffered but we were able to manage quite well and I felt better. But still it didn't feel like I wanted."
Honda informed Marquez that Vinales had crashed via his pitboard, though the reigning champion said he had already seen a replay of the incident on the video screens.
"It didn't change my plan, which was to try and understand the situation," said Marquez when asked if knowing Vinales was out had influenced his subsequent riding.
"The mistake of Argentina was big and I didn't want to repeat it."
Read the original article on Eurosport: Honda has 'problem' to solve despite win