As stated in the first section of Rule 16, the purposes of the conference is to accomplish any of the objectives listed (specifically section C(2)). The court will direct parties to attend this conference and participate in good faith to achieve a more efficient path through the end of the discovery process and up to trial. Any party called to participate in the conference may raise the issues listed within this Rule, but the Court will also have their own standard issues that they address at every conference.
If there is a particular subsection of Rule 16 that you wish to raise yourself (or through your attorney), this conference is where it is brought up. There is no need to make any motion or draft any other writing prior to the hearing in order for a particular issue to be discussed. The judge, when necessary, will then reduce any agreements or decisions made at the conference to a pretrial order.
Let me know if this addresses your concerns or if you have additional questions.