I am a facilitator in Missouri, so can only speak to how facilitated IEP's are conducted in my state, but I agreed with Jenna that all you need to prepare is a letter (or email) of parent concerns. In Missouri, I speak with both the parents and the school district via phone prior to the meeting. In my phone conversation with the parents I try to pull out all concerns that they have. I also offer to draft the parent concerns letter is they are unsure of how to do this. I, of course, have them review and approve the list. After parent approval, I forward a copy to the school district. It makes the process go a little smoother when the district is aware of the parent concerns prior to the meeting, as is the case with any IEP meeting.
The meeting itself will most likely be conducted similarly to a "regular" IEP meeting. In fact, the facilitator has to follow the agenda outlined in the IDEA. There will just be some extra "bells and whistles" in the meeting such as visual charts that the facilitator (or someone he/she asks) tracks. The neutral facilitator will only jump in if tensions are rising, the meeting is getting offtrack, pros and cons need to be developed to reach a consensus on a particular proposal, etc.
As for a report and what is done with the information at the end of the meeting, in Missouri there is no report generated after a facilitation. The school district is allowed to take pictures of the charts if they do so with a school device (not their personal cell phone) for purposes of adding it to the student's file. They charts are then taken down and destroyed.