Jora really summarized a lot of great points.  I might also add that it is best if you can have some break-out sessions so that you get maximal participation.  Situation diagramming is an excellent way to engage your partners and team members, so you want 100% participation that usually is only possible in small groups.  You need a facilitator with each break out group.  It might be helpful to also have the big questions you will need to ask over and over again like "What are the direct threats that alter your key ecological attributes?" and "What are the proximate underlying causes of those threats?  Be specific!" on big flip chart paper so everyone can continue to refer to them as it is so easy to stray.  Getting a good grasp on those direct threats is very important as it is easy for the group to start getting into the big picture (i.e. population growth) and catastrophizing.  I would continue to come back to those threats and do frequent gut checks to make sure everyone still agrees that they are the most direct threats and the right threats.  In order to do a round up for the next day, I would have a sticky dot vote and discussion around what the very high and high threats are so that your strategy discussion can be focused on abating/mitigating those threats.  Ideally, if the facilitator has time, you would clean up and enter the work of the group into Miradi or Visio that night, focusing on the high and very high threat branches of the diagram, to ensure you can get to the heart of the strategies discussion the next day.