Nothing is more important in custody litigation then to get what you have bargained for. Although at the time of such negotiations you will be anxious to compromise and reach an agreement in order to avoid the emotional trauma and expense that a trial will entail, you must consider that unless you have provisions in the agreement to accommodate a change in circumstances, you will have a tough time to convince the court that a change is in the best interest of the children and that a significant change has taken place.
When a prior agreement has been reached, and the provisions are incorporated but not merged in the decree of divorce, the surviving agreement will be treated as a binding contract, except the provisions relating to child custody or visitation which is subject to the court's determination that the initial agreement was consistent with the children's best interest. Of course if fraud is involved or the agreement is unconscionable on other equitable grounds asserted, these agreements may be set aside. Change is sparingly granted by the courts and the facts presented must be persuasive and capable of but one outcome. Statistically, less than 10% of such application will be set down for hearings and the ultimate relief granted after trial.
With this knowledge in hand, and the fact that the courts will generally give custody to the parent who was first awarded or obtained custody by voluntary agreement or court order, before agreeing to such provisions you must carefully consider the long term effect that these determinations will have when a change of custody or visitation is sought. Without an evidentiary showing sufficient to warrant ahearing, your application will be denied based upon the papers submitted. The only remedy remaining would be to appeal the lower courts adverse determination to an appellate court for review.
It is also to be noted that the appellate courts are loathe to make a change to a pendente lite (pending trial) order inasmuch as they will normally hold that there must exist exigent circumstances to consider doing so. The explanation given is usually that any perceived inequities can be remedied by a speedy trial where all circumstances can be fully explored. See Stock v. Stock, 2013 NY Slip Op 05307.