1. Mother is the natural guardian of children up to their 5 years of age,
2. So, in normal course, your wife will get their custody,
3. However, welfare of the child is considered as of paramount importance while deciding about his/her custody,
4.So, in your case, if she marries her BF or starts living together with him, you can file a child custody application seeking their custody on the ground of their welfare arguing that their welfare will be jeopardised since their mother has married someone else and they will be better taken care of by their father who has not married.,
5. So, you can file the child custody case after availing MCD from the Court and waiting till she marries her BF or starts staying with him.