Child custody while having them

Do I need to file for child custody when I already have them? My son is 3 and half years old and my daughter is 8 and a half years old. My wife left matrimonial home about in May 2016. I filed for divorce in July 2016. My wife had left matrimonial home with both kids in May 2016. But in June 2016 returned my daughter. And in September returned my son in the presence of the elderly people of both sides in the court premises unofficially. And I also have the photographs of the same. Immediately after returning my younger kid, on the very next day, she started calling me and threatening me that if I don't return the kid immediately she will file a kidnap case against me. And after four day she thronged at my house with four other people to take the kid away forcefully. But finding my house locked they made nuisance in the apartments. I got the information and I immediately called the local police station. The police called them and warned them not to do so again. On 22 September 2016 I filed a complaint against my wife and her brother and the police has given me a receipt for the same. They have not filed FIR but put it in record. On 4th October, my wife again barged into my home and tried to carry away the younger kid. But was rescued by my parents and also the police and me arrived home in 30 minutes. It took the police 1 hour to counsel my wife again and she left. The police told her that if she intends to see kids she can apply for visitation or come to the local police station where they will make arrangement to see kids. But since 4 October 2016 she has never returned and never shown any interest in the kids. Later she filed 498A and 125 Crpc in her home town. The kids are happy with me. I have got medical documents to prove my wife's psychological illness. And also of Psychologist about the condition my kids were when she returned from my wife's place. Now she is trying to get visitation from 125 Crpc Judge or file for custody in her town. Do I need to file for child custody at my place though I have the custody of the kids for over six months? Do I need to file under GWA? Please suggest...