Throughout the series, Kyo and Kisa rarely seem to interact. When she first appears to Tohru and spends the night, she ends up picking her favourite food for dinner: niratama (a leek and egg dish). Kyo grits his teeth in annoyance but doesn't really protest for Kisa's sake.
Later, when Kisa next comes over to visit, Kyo calls her a brat and is chastised by Yuki for being insensitive. Kyo says he doesn't care if Kisa is scared. Kisa looks a little saddened by this but she's seen smiling when Kyo is being teased by Shigure for flirting with Tohru.
Most of their interactions seem to be around Tohru and we don't really see them talk to each other much until the very end of the series when Kyo has just come from his biological father's house. Kyo is throwing up from the tension when Kisa and Hiro walk by. Kisa seems concerned for Kyo and offers him a handkerchief. When Kyo looks at her, he sees Tohru and feels that the two are much alike. He thanks her and she offers to help him clean up his sick. Kyo's taken a back (probably grossed out) and says he'll do it himself but Kisa and Hiro go off to borrow cleaning supplies regardless.
They meet once again at the final banquet but we don't see them interacting during the brief time they're there.
I guess since Kisa loves to stay close to Tohru, she probably does interact with Kyo a lot more than we get to see, especially after the series is over. I can just picture an older Kisa babysitting their children. <3