McManus, on loan from Middlesbrough, has strained ligaments while Skuse will undergo surgery shortly on a fractured cheekbone - both sustained their injuries in Tuesday night's 2-0 defeat at Birmingham.
Louis Carey, however, got an hour of football under his belt in a reserve match so he provides another option along with defender James Wilson.
And manager Derek McInnes hopes the fact his side play on Sunday will improve the chances of top scorer Steve Davies returning to action. The Scot is touch and go for the home clash with Charlton and his return would be a huge boost for struggling City.
McInnes' side have lost their last six games and are now just a point and a place above rock-bottom Ipswich.
Charlton will again be without a host of players with defenders Lawrie Wilson, Cedric Evina and Rhoys Wiggins, and strikers Ricardo Fuller and Yann Kermorgant all still in the treatment room.
Wilson will be out for a couple more weeks with a thigh injury, Evina faces a lengthy spell out with a knee problem and Wiggins is some way short of returning from a foot injury.
Fuller is still troubled by a hamstring problem and Kermorgant is another long-term absentee after breaking his ankle.
Boss Chris Powell could welcome back Jordan Cook, however, after he missed Tuesday night's epic 5-4 win over Cardiff through illness.
Fellow forward Danny Haynes lasted 68 minutes on his first start of the season following hamstring trouble and should be involved again.