Bafana coach Stuart Baxter recently roped in Madisha as a replacement for suspended Kaizer Chiefs defender Erick Mathoho, while Mothiba earned his maiden call-up for Saturday's 2018 World Cup qualifier with Burkina Faso at FNB Stadium.
Mothiba returned home with confidence after netting a match-winning hat-trick for Valenciennes against Orléans last week. The 21-year-old, who represented Amajita at the previous Olympics, is on loan at the second-tier outfit from Ligue One side Lille.
"Madisha has been around for quite a while, this is not his first camp. We have been together in previous camps," said Khune when asked how the pair are doing.
"Lebo, I've played with him in the U-23s at the Olympics, so we have got a great understanding.
"I mean they've settled in well. We have got senior players like Morgan [Gould] and Andile [Jali], who have been very helpful to the other guys that just came in.
"So it is very important that we all motivate one another. It's not a matter of seniors and juniors, we are all in the same boat and we'll have to deliver on Saturday."
Khune, an overage player at Rio 2016, has eased fears he could miss the clash with the Stallions through injury.
Bafana are bottom of Group D with a point from three games - five points shy of the pace-setting Burkinabe and Cape Verde, who have both played an extra match. Senegal have five points from three fixtures.