She's All Class, a brilliant winner of the Wyong Magic Millions last month, held her price at $4.20 despite drawing a horror gate 18.
Waterhouse and Bott have been training together for four years and have never struck Magic Millions success.
However, Waterhouse is shooting for a fifth Magic Millions Classic after claiming it when she trained solo with Driefontein (2012), Dance Hero (2004), Excellerator (2001) and Assertive Lad (2000).
Bott believes barrier 11 was a suitable draw for Swift Witness, who is a daughter of Star Witness.
"Midfield is a good draw for us," Bott said.
"She's got enough tactical speed to be able to lead if needed or she can take a sit like she did at the Gold Coast on Saturday.
"It's an ideal draw as we can assess the pattern of racing on the day before deciding the best way to ride her."
Swift Witness was placed on debut behind She's All Class in the Wyong Magic Millions before rocketing into Magic Millions calculations with an easy three-length win in the Aquis Gold Pearl over 1100 metres at the Gold Coast last Saturday.
"It's fair to say she's closed the gap on She's All Class who had the benefit of race experience over us at Wyong," Bott said.
"She's All Class is still the one to beat and I've got huge respect for her.
"She's probably improved since her Wyong win but so too has Swift Witness."
Lindsay Park's bid for a second Magic Millions Classic victory also suffered a major blow when Finance Tycoon drew barrier 21.
Finance Tycoon won the Group 3 Maribyrnong Plate over 1000 metres at Flemington at his previous start before the Lindsay Park operation sent the son of Written Tycoon to Queensland.
Lindsay Park has won the Magic Millions Classic only once with Catnipped when the late Peter Hayes was head trainer.
Finally, the Tony Gollan-trained Isotope remained a $2.80 favourite after drawing barrier seven in the $2 million Magic Millions Guineas over 1400 metres.
His biggest threat, the Ciaron Maher and David Eustace-trained Away Game, drew ideally in barrier three and is second favourite at $3.80.
Away Game was runner-up to Isotope in the Listed Gold Edition at Eagle Farm last start and is aiming to become the first horse to win both the Magic Millions 2YO Classic and Magic Millions 3YO Guineas.