First, a solid WBS needs to be created to define the entire program down to the Work Package level. Project’s WBS field is lacking in flexibility, so you might want to use a custom field. The entire aircraft systems and sub-systems, including sub-contractor work needs to be incorporated into the WBS (flight controls, structures, avionics, electrical design, engines, cabin systems & etc.).
Are you planning on using earned value and/or tracking cost? If so, this further highlights the need for a good WBS. And, the labor charging system needs to be aligned with the work packages to which labor and material costs will accrue.,
Secondly, how large a program is this (rhetorical question as the answer is none of my business)?. You will have to make a determination on how large your master schedule will be.
Third, all IPT members must be included in planning process for scheduling development.
I know from experience how large an effort this is. If EV/cost management/labor tracking is involved and the schedule is lookinbg like it is going to be very large, I would propose re-assessing which scheduling tool you employ, and highly recommend bringing in scheduler(s) as consultants/contractors who have this specific experience.
There are very unique and complex aspects to aerospace development, and I am suspecting that your question is the tip of the proverbial iceberg.