On very rare occasions, I get to write big fancy reports (or long, complicated chapters for those reports) that don't fit in a specific format and can't just be copied over from an earlier report/another project. The very first thing I do is write an outline with suggested numbering for subsections, figures, tables, and appendices.
The second thing I do is grab all potential reviewers/managers/section writers and arrange for a big meeting to agree to the organization. Do you want to organize this discussion by contaminant type? By area? By process? Have I missed some critical piece that will need to fit in? Most of the time, the people involved couldn't care less, and so they breeze through and agree with everything I say just to get the meeting over with. I try to be a stickler on this, and if there's any potential disagreement with the overall format/plan for the report, I try to get client buy-in.
Once I've actually started the meat of the analysis, I may need to rearrange some things. So I don't fuss with the exact numbering/formatting until bulk of the text is together. If I discover some and major new issue with the geology or an unexpected chemical trend, I'll try to check in with the decision makers to adjust before spending much time on the write-up.
It is infinitely easier to have an approved plan of attack, than to write 40 or 50 or 200 pages and have someone say, "nah, I want to put it together this way" and have to re-write everything. And renumber the tables and figures and appendices and change all 400 references to them. And of course, with big reports, inevitably you only get those "re-write everything" comments once the whole thing is together for final review and you have to change everything at the last minute and that's when critical pieces fall through.
I generally take technical/writing criticism well. I promise. I do not take constructive criticism quite as well when I'm told to totally reorganize a completed thing ages after I tried to get initial buy-in on the organization and was ignored.