opaque building envelope construction

The helpful notes tell you what should be entered in the opaque assembly tab for roof in the MEPC. The building ID is the project name. No you don't have to enter all the zones. You need to enter different roof assemblies in certain situations such as residential, or non-residential; conditioned or semi-conditioned; and new vs existing. If you have multiple buildings and the roof assemblies are different then you would need to enter each one and indicate where it applies. No need to enter a roof for each building unless there are differences.

Depends on how you modeled it. If you have multiple roof assemblies in your model then enter each one in a separate row in the table. If you have done some sort of weighted average then provide those calculations in a separate document.

It should include all of the assemblies used in your model. Each one should include a thorough description of the assembly and a reference to the 90.1 Appendix A table used to determine the whole assembly U-value or a reference to another similar method. It should include the U-value. Yes that applies to walls too. I am not aware of any instructional materials beyond the instructions embedded within the spreadsheet itself.