The multi-threat Kaepernick, who gained a record 181 yards rushing in his first NFL playoff game this postseason against Green Bay, runs a read-option package that has kept defences guessing on whether a run or a pass is coming.
"Any time you play option football, somebody has to have the dive, somebody has to have the quarterback, somebody has to have the pitch," Pees said on Thursday.
Pees said communication between the defenders and the understanding of their assignments before the snap was critical given the success the strong-armed Kaepernick has had.
Veteran Ravens safety Ed Reed said the various options could lead to confusion.
"You have so much that can come off it," said Reed. "You got the pass off it, you got the option off it, you got the dive off it, you got the quarterback off it. They might deliver a pizza or two off it, you just don't know what they gonna come with."
Pees said he had faith in the Ravens' plans to contain the 25-year-old Kaepernick, but admired the skill and enthusiasm of the big, fast San Francisco signal caller, who will be making just the 10th start of his NFL career.
"I hate to say this, since I'm defending him, but he's actually fun to watch," the Ravens coach said. "He looks like a kid that just wants to pick up a ball and go out and play in the backyard in a pick-up game. He's done a great, great job and he looks like he's having fun doing what he's doing."
Linebacker Ray Lewis, a 13-time Pro Bowler, said in their film study the Ravens found flaws in how other teams attacked the option plays.
"A lot of people who played against them just never communicated at all," said Lewis. "I believe that's one of the advantages of what we have as a defense.
"A lot of people against the read-option just played as individuals. It's really hard to play that type of package as individuals. You have to play it as a group."
Pees said the Ravens would vary their assignments to disguise how they were defending those plays.
"It could be a defensive lineman, could be a linebacker, could be a secondary guy," he said, again stressing communication and execution. "Everybody needs to know what they've got before the ball is even snapped."
"You never play anything the same way. You always have to have change-ups all the time."
Anticipating the strategic chess match ahead of the game is one thing, and adjusting during the game is another.
"I'm sure they're going to come up with something new over the two weeks," Pees said, noting the extra week off since the conference championships. "Just like we probably will."
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