Thank you for your question.
You can explain to the court when you argue the motion that the custody order has already been addressed. It is easier to have the court take an issue off its calendar than to put one on its calendar. The only issue is that by bringing up the custody issue, you may be giving the other party the ability to bring a motion opposing custody. If this happens, you can file a reply to the opposition papers explaining that it was in error that you requested that custody be discussed and that the only issue you desire to be adjudicated is support.
Your other alternative is to file amended paperwork now, not giving the other side the ability to respond to the issue of custody.
If you don't feel the other side will file opposition papers or there is no opposition, then I would just wait and address the issue with the court when you are arguing the motion. However, if you know that the other side will vehemently oppose every issue in the papers, then you may consider filing an amendment as soon as possible, so the other side does not necessarily have the ability to respond to the custody issue. (The fear is that depending on how long ago the court ruled on the custody issue, if the opposing side makes a compelling argument, you may not be able to stop the court from considering it once the ball is rolling.)
Please let me know if you have any other questions, or require clarification of this matter. Otherwise please hit "ACCEPT", so I may receive credit for my response. Tips and feedback are also appreciated.