I break my rules down by situation on offense and by defensive formation. Offensively I have rules for deep in my own end, deep red zone, 2 minute drill, 1st down, 2nd and 5 or less, 2nd down 6+, 3rd and short, 3rd and medium, 3rd and long, 4th down rules for specific situations, and rules for late 4th qtr whether ahead(run, run, run) or behind (pass, pass, pass).
I would like to get more specific offensively, but no time.
Defensively I have packages combining normal/nickel formations, nickel/dime, nickel/dime/quarter, normal/nickel/dime and separate them into down/distance. I also have red zone defense rules and a prevent package.
When I gameplan, I sort of do what you did Booger, I chart plays by formation. Based on that info, I then decide which defensive package I want to use against my opponent's 1-1-3, etc.
I also try to have my matrix match the rules as close as possible, if not, things can go haywire. This sounds complicated but it's not really. I can do a game plan in about 15 minutes if I'm not changing the plays I run. I prefer to keep the same plays each game while simply changing how I use them.
My biggest issue is when I need to change up my plays defensively. For example if I switch a 1 deep man play to a corner blitz, it messes with my rule percentages and matrix. I try to keep changes within the same group, changing a 1 deep man play to another 1 deep man, or offensively changing a short pass in the 1-1-3 to a different short pass in the 1-1-3.