I agree with High School Parent's response that your son's age is relevant to this discussion, and that at some point his supports should be reduced and he should take charge of own organizational system. However, it doesn't sound like that is what is going on here. He should not be in charge of data collection for his IEP. Data collection and progress monitoring falls under school district responsibilities, not the student's. Again, I agree with High School Parent that if he needs something for "self-monitoring," a specific goal should be stated for this.
Finally, given that neither your son nor you understand the daily note card system, what he is supposed to do with it, and why he is doing it (it can't be for data collection or self-monitoring for reasons given in first paragraph), you need to request an IEP meeting to seek clarification on these items.