As a computer engineer by day (and a musician by night :D), I prefer writing small parts and then, connecting them together. Like "modular programming". In my personal opinion, it doesn't matter where you start.
When I started writing music for a group of instruments, I just started writing metal music. Metal is easy, specially when you don't know music theory, you only read tabs from great bands (i.e. Metallica) and then, start copying them. But when I learned music theory (the right way, of course) I wrote metal songs again, because now, I didn't need to copy metallica or any
ther famous band.
But why it's important? When you write a metal song, the most difficult parts are bass and guitars. When you wrote them, everything else is written by itself (I call this "Black metal logic"). Imagine the orchestra is your band. Which part is the most difficult for you?
Of course, it is!
So, the way I write orchestra is :
1. Writing for bass instruments
It helps a lot. specially when you have the ideology "one chord per bar". Even if you want to use more than one chord in a bar, it will help. But why? Because in every bass instrument, I add the root notes. sometimes in "double bass" section, I add the fifths.
2. Writing for Viola and Clarinet
The second part I start writing. I just add thirds of the chords. When I finish this part, I have idea about what chords I used. For example, I have "C" in Cello section , and "E" in Viola section, then I know I have a C major chord there.
3. Writing for Other Instruments
I just write some melodic lines, which includes main notes of the chords (depends on the chord type), for every other instrument, but melody isn't written yet.
4. Writing Melody
It depends on you, but I prefer trumpets or violins playing my melodies. Sometimes, I may even write this part for a solo guitar (Have you heard Yngwie Malmsteen's Concerto Suite?) and make my orchestra a concerto for solo guitar.
I hope I could help!