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Defending champions Bayern, who also won their eighth successive Bundesliga title last month after Flick rejuvenated the squad, face a Leverkusen side who are in their first cup final since 2009.
Flick, who took over as interim boss in November when Bayern sacked Niko Kovac, will be competing in his first final after being named permanent manager in April.
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"We know they have enormous speed in their team. We've adapted for that," Flick told reporters on Friday. "It worked well a few weeks ago in Leverkusen, so we're positive it'll work again tomorrow."
Bayern, who lost 2-1 at home to Leverkusen in the league in November, managed to win the return fixture 4-2 last month.
"Our team has developed strongly on the defensive, we are better," he added. "We have to find the right ways to face the speed of Leverkusen.
"I was happy with the team's performance in training this week. The quality and intensity really pleased me... We're playing against a team who can hurt us with their strengths. We have to be focussed going into the game."
Flick said Bayern midfielder Thiago Alcantara has recovered after having groin surgery and was "100% fit" to start.
"Thiago's operation wasn't that long ago, but all our plans have worked out," Flick said. "He's handled the full workload since Wednesday, so can play from the start on Saturday."
When asked about media reports linking the Spaniard to Liverpool, Flick said: "I hope he won't go."
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Leverkusen's fortunes have hinged on Kai Havertz, the 21-year-old midfielder with 16 goals and nine assists in all competitions, leading to questions about his own future at the German club with several teams linked with his signature.
"He's important, but he cannot win the game alone," Leverkusen boss Peter Bosz said. "I don't think the game has anything to do with his future.
"We will do everything within our power to win the title. Absolutely, we have a chance... We also have to be realistic, they have a really fantastic team.
"If we show the mentality to really, really win this title, I think we have a good chance to beat them... In November, we showed them that we have a good team and we can beat them."
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