The first thing you need to do right away is send a parent concerns email. Send it to the entire team that is listed for attendance at the second meeting (it's not necessarily a bad thing that the deputy director of spec ed is coming - he/she might know the law better and keep the "IEP Facilitator" in line so you can speak, people might not leave the meeting, etc.). I don't know in what category your son was found eligible, but make a list of all the concerns you have for him in the educational environment, including behavioral, academic, social, etc. It's best to base this on data, so look at the evaluation the school did to come up with ideas, but you can list whatever you feel is appropriate. If you disagree with the school's evaluation (for instance, it says he is at grade level for reading and you don't think he is), ask for an Independent Educational Evaluation in all areas you disagree with in the school's eval. (They will ask, but you don't have to give them a reason for why you disagree.) If there are some areas that the school did not cover in their evaluation that you think they should have, request additional testing.
Think about how long you think the second meeting will take. Then reply to the Notice of Meeting (and add all attendees if they are not on the distribution list for the notice you received) and state that you request a time frame of _____ and confirmation that all participants can stay for the entire meeting and if not, to reply with a time they need to leave (if it's the OT person and OT has already been discussed, for example, you can agree to their leaving the meeting early). You might consider recording the meeting (which also keeps people "in line" and gives you documentation that you weren't allowed to fully participate). This depends on how "nuclear" you want to go with the school, because this will be off-putting to them. Make sure to look up your state's laws on recording (if it's a one party state, you don't need their permission to record). But also look at their district policy on recording - some districts do prohibit it in a policy. If you decide to record, you could either state that in your reply to the Notice of Meeting or "surprise" them at the meeting. (Some state laws and school district policies require so many advance days notice if you plan to record the meeting.)
It's good that you received the second draft prior to the second meeting (I would have suggested asking for that if you hadn't). I would ask for a Prior Written Notice (PWN) on everything they refused you in the first meeting. If they reply that the second meeting is continuation of the first meeting and so all will be reflected on the PWN following the second meeting, that's fine. Just make sure you get that in an email reply and not a phone call (for documentation purposes).
At the meeting, ask that your parent concerns email be copied and pasted and put into the IEP document under "Present Levels." They may refuse. If they do, ask right then that this refusal be noted on the PWN. Have your parent concerns list printed out and with you so you can check off each item as it's discussed. If an item isn't discussed, bring it up. Take your time to be sure - don't let them rush you through the meeting or the double-checking of your list. You have the right to do this. After every item they refuse, ask it to be put on the PWN.
Since it sounds like in your state the IEP will go into effect after 10 days with no signature required, make sure that you receive a PWN after the meeting that lists ALL the things the school district refused to do. If it doesn't, request another PWN that does. Do EVERYTHING in writing.
And you are absolutely correct - the team should be COLLABORATING on the IEP document. You as a parent, specifically, have a right under federal law (the IDEA) to have "meaningful participation." Don't let them take that away from you.