Changes to an incorpoated sep agreement

If we incorporate our agreement, and wish to mutually make changes, such as to visitation and/or child support amounts, would we still have to file motions with the court or can a second notarized agreement supersede what we had incorporated?

Oh and if our signed agreement right now specifically asks that it get incorporated and our county will do that, what is the chance the judge will not allow it if one party changes their mind on the date of court?

If you want to make changes to the agreement, you can both execute a modification. If you have it incorporated, you would then enter a consent order to modify the agreement. If the agreement states that it will be incorporated, it should not matter what the parties desire at the time of the entry of the court order, but what was in the agreement.