The Gresini rider ended Friday's running at the Algarve International Circuit safely through to Q2 on Saturday after finishing third in second practice.
But Marquez did register his first race weekend crash on the Ducati when he slid off his GP23 Ducati at Turn 5 while pushing on his final time attack lap.
Marquez says a "small change" to the bike gave him more confidence to push, but when he lost control of the Ducati under braking his "instinct" for riding the Honda took over and led to his crash.
"We did a small change on the bike, it gave me more confidence," Marquez said. "If you have more confidence, you are able to push more and step by step we need to go in that way.
"The crash, for example, was on the time attack, on the last time attack, and as I said yesterday when I was behind somebody with Honda I felt better.
"With the Ducati, I feel worse. So, it's there where I try to manage in a new way. I lost the rear on entry, it was a strange crash, but in the end, I did a mistake and I need to analyse well. I think I know why I crashed."
He added: "As I said to you, when I do time attack my instinct arrives and then I was used to going super-fast on the apex with the Honda with some sliding.
Watch: MotoGP: What we learned on Friday! | 2024 #PortugueseGP
"With this bike, you need to ride in a different way, the potential is in another area.
"In that braking point I had the shaking on the first part, and then the speed was too fast but I tried to go in with that instinct with some slide. But now we know that I can't."
Despite this, Marquez says he is "enjoying" riding the Ducati in Portugal and feels it will be "easier" to manage a race distance this weekend than it was in Qatar.
"Easier than Qatar," he said when asked how he thought managing a race in Portugal will be.
"In Qatar I was struggling a bit more. I was riding some of you would say conservative, but I was just riding without confidence.
"And it looks conservative, but if you don't have the confidence you can't push.
"So, here the confidence is better. Also, Frankie [Carchedi, crew chief] starts to understand better my riding style, I start to understand better the bike and we did a small change on the bike.
"I start to know what I need on the bike to be fast. And all these things help to have more confidence and be faster on the lap times. And especially be quick on the times, which is one of the most important things on the race weekend."
