Story Cubes: DS will now throw a fit if he even sees them, so no, we haven't used them. We've worked on some of these skills through other means, but encountering a lot of resistance. The summer successes are getting him to read fiction he hasn't previously read.
DS' math metacognition is .... weird. It's not clear to anyone that DS has actually learned any new math concepts in school yet. What he does learn (under duress) is how to cast what he already knows into a school-appropriate form. I personally view this as important skills, and showing ones work serves more than just "because the teacher wants it." Our hope is that these skills become more automatic, and eventually he will be able to prove with more that just the right answer that he has intuited math that hasn't been instructed. To me, it's all about being able to lay out a logical argument, which should be applicable to any situation.
We are fortunate to be in a very different situation as you with regards to the school. Yes, I meet with the teachers before school starts because everyone in the school is on board with helping DS succeed and progress on his weaknesses. I'm meeting with the principal and DS's homeroom teacher tomorrow. The agenda is to sort out a few concerns, and to give the teacher a head start on understanding DS. DS is also on an IEP, which gives us a solid frame work within which to address the exact issues you're sorting through: handing in homework with work shown is part of his IEP, and it's separate from performance on tests. Seeking help as appropriate is also an IEP goal for him, under his EF goal.
In your situation, if this teacher seems receptive, I'd ask for a meeting with a collaborative tone: "DS is on a 504. This subject is an area of intense interest, and I anticipate that this class could be an experience where we see a huge amount of growth -- or he can end up irritating everyone in the room. I'd like to meet so that we can figure out a way to make set the year off in a way that he learns appropriate classroom discussion skills." It puts it right out that you know your kid isn't perfect and that you want to work together.
