You need to be separated for at least 12 months before you can pursue a divorce. Once that 12 months has passed, you can file either jointly or solely for a divorce through the court.
In regards to children, you'll need to first attend a family dispute resolution conference with the father to try and negotiate suitable parenting arrangements that meet the best interests of the children. You will not be able to pursue parenting orders unless you attend family dispute resolution. You can contact Legal Aid or Relationships Australia to discuss this.