Assuming the DVO application has been successful and includes the children as named parties, I would suggest that your partner start the process for parenting arrangements, but stay away from the ex and the kids in the meantime, to avoid complicating matters further down the track.
The first port of call is mediation, or family dispute resolution, in order to try and reach a parenting agreement that enables the kids to spend time with both parents. If this agreement cannot be reached (and even if it can), your partner will receive a s60i certificate, which is necessary to begin court proceedings.
If it goes that far (and most don't), a court will decide care arrangements based on what's best for the kids, with secondary consideration given to the level of involvement your partner has had since the kids were born and following separation; whether or not your partner has fulfiled his financial obligations to the kids; whether or not your partner can provide for the kids' emotional, physical and mental needs; etc. All of these considerations are outlined in s60CC of the Family Law Act 1975.
There is a necessity to protect kids from family violence, however it is worth noting that a domestic violence order alone is very rarely enough to convince the court to oust a parent from a child's life. The other party will need to show that there is a pattern of behaviour which endangers the kids, either physically, mentally or emotionally. Summarily, parenting orders override domestic violence orders, but said parenting orders still must be made in such a way that they consider the domestic violence orders. How this is achieved is a matter for the court to decide - sometimes, it's time with the kids at a contact centre; sometimes it's time supervised by a family members; it varies.
It's impossible to predict an outcome from the court, but given that the kids haven't seen your partner for three years, I wouldn't say it's unlikely that your partner could be looking at a gradual increase in time spent with the kids over the course of a year or two. I say this because I have not often read a decision whereby the court orders 50/50 care after a long period of no contact because doing so is considered too stressful for the kids.
However, with that said, it's also dependent on how old the kids are. If considered old enough and mature enough to make informed decisions about their own care arrangements (usually around 12 years of age, but there is no law which states that), the court will take these into account and give them substantial weight in the decision.
When your partner attends family dispute resolution (which may be with or without a solicitor), he may want to consider all of these things when negotiating care arrangements, particularly the one about gradually increasing time the kids spend with him.
I hope this has helped.