The way to make so complex scenarios is to have a very CLEAR idea of what do you want, and how can it be made.
The first thing is for the chosen
I have started a lot of scenarios, specially campaigns because that's what I like much, but I allways fall onto my own improvisation. Sudently I say "why not placing a neutral ship here?", "hmmm a chinese Kilo at 2 knots would be interesting for next missions..." and that sort of things makes my original idea to sink.
Another thing that ruins my missions is to make various changes at a time when I discover a mistake when testing them.
The second thing is a matter of trying, and trying, and trying... and asking here to the ones who knows.
That's why I only have achieved to make one campaign... and had to make it very short because I run out of ideas...