In a U.S. Government RFP, the instructions will typically be in Section L. If you do not have a Section L, you will need to look elsewhere for the instructions. If the RFP does not have a section providing instructions, you will need to look for language describing their expectations regarding the structure of the proposal.
The first step in building a compliance matrix is to create the high level outline. This should be based on the instructions in the RFP. In the first column you should enter the proposal heading, and in the second column you should include the RFP reference.
Start by identifying the volumes and sections that the customer expects to see. If they provide a description for what should go into a section, you must decide whether to create subheadings for them. Each heading that you add to the outline, should contain a reference in the Section L/Instructions column so that you know which headings are required by the customer and which ones were optional or ones that you created.
When you have completed adding the instructions to the compliance matrix, you will not only have your high level proposal outline, but you will also be able to verify that you have followed all of the instructions in the RFP.
If the instructions include a narrative description of what the customer wants to see in your proposal, then you should add headings as needed to your outline until you have a place to address everything the customer has asked for.