You do not have to agree to the change of custody. Why hasn't he paid until now? Doesn't he have a huge arrearage he owes you? He should be paying on the arrearage in addition to current child support. You need to consult an attorney.
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If there is a modification of custody, then the child support order would likely be modified. It doesn't sound like the change of custody is really your idea. You do not have to agree to any change of custody. The non-custodial parent would have to prove by clear and convincing evidence that a modification of custody is necessary for the best interests of the minor child. Splitting up children is rarely done.
If there is split custody, usually the child support would be offset - He'd pay you 28% for two children and you'd pay him 20% for one child. However, the court has wide discretion in such a situation to set support as it deems equitable. Neither you or your ex modify support -- that is a function reserved solely to the courts.
You state there is a child support order. You also state he just started paying. Was that order in place for a while before? If so, there may be a substantial child support arrearage (and interest) that is owed. You should probably contact an attorney with more information for a more precise recommendation.