If you're wanting to seek custody, but the other party doesn't agree to the modification then you will have to prove to the court that there is a "change in circumstance". This would be a reason you believe the court should change custody to you, from the other parent. If you can prove a change in circumstance, such as abandonment, child neglect, danger to the other parent, or child or siblings then you have good reason to request a modification, and your arrears would not be a reason to stop, or deny that.
Custody is in the best interest of the child.
I am already involved in a custody issue, and I am behind about $2000 but pay $30 extra a month on top of what my court order payment is, towards the arrears, and my attorney has told me that is not cause for denial.