He is also wary of Melbourne ahead of Friday night's clash at GMHBA Stadium, saying their best can be daunting.
Stewart was a late withdrawal from last-week's loss to Brisbane with a knee injury and Mannagh (foot) will return for the first time this season.
"He'll play, unless something we're not expecting happens in the next 24 hours," Scott said of Stewart, one of Geelong's most important players and their backline general.
"He was very close (last week), which gave us supreme confidence that he'd be okay and nothing changed in his training earlier in the week ... to alter that thinking."
Scott said Mannagh had been out of the AFL team for a little longer than he would have liked.
Fellow forward Shannon Neale (ankle) will also play, but midfielder Mitch Knevitt is out because of a foot injury and Jhye Clark was dropped.
The winless Demons made four changes, three of them unforced.
Kozzy Pickett will return from suspension as the Demons also recalled Caleb Windsor, Daniel Turner and Charlie Spargo.
Out-of-sorts forward Bayley Fritsch retained his spot, but Xavier Lindsay is out with a knee injury and Jack Billings, Aidan Johnson and Blake Howes were dropped.
After demolishing Fremantle in round one, Geelong have suffered narrow losses to St Kilda and Brisbane.
"It's been pretty good, just good enough. We think we'll get better," Scott said of Geelong's start.
He added it was crucial to strike a balance between fixing their problems and not overreacting "and almost having this self-perpuating negative cycle.Â
"We're not going terribly. I mean, I could make the case that Melbourne aren't either, but that isn't going to get much support."
The Demons are in early-season strife at 0-3, with smackings from North Melbourne and Gold Coast.
"For all we know, Gold Coast could be the best team in the comp. You could make a strong case that's true. That puts their performance last week in perspective," Scott said of last weekend.
He added Melbourne at their best is very hard to stop and their players are "daunting at times".
"It's just poor policy to be looking at a team, thinking 'they have some weaknesses that are just going to persist'," he added.
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