i was thinking that if i take back the car, i will pay him back the rm15k deposit that he paid initially. But do i have to pay back the past 1 year installment that he paid off? Or those are consider as the "rental" during his possession of driving the car for past 12 months?

It is my huge mistake when i decided to help him but he seems to taking advantage of my credit rating and causing a serious mess up with my CCRIS... i will take to him and have a clear cut to any financial related stuff from me. 

Just sell the car. If got extra, give him back. If need to topup, ask him / his family to settle. If they can't, you settle it and take the loss as lesson learned.