As a generic point about using large templates, it's really up to you which way you organise yourself. I use folders too, for big layouts, and it seems to work ok. For a quick draft however, i use a simple layout with 4 or 5 articulations per section (strings) put through Kai's performance tool, lashed to a selfbuilt soundbank that lets me work at speed, and doesn't tax the laptop too much. And as i do 90% of my work now in Logic's score editor (cos i learnt much recently, lol) I've hooked the performance tool up to show in the score editor as a 'real score.'
If i'm then to go to work on the nuances at a deeper level, i then export the midi to one of 4 orchestral templates (by section) and concentrate on getting the best sound i can with what i have.
This seems like a convoluted process, but i would think with VI's, you could scale this down considerably, and the option to have a 'real score' with switched artics would be extremely useful.
As a matter of interest, can you assign keyswitches to your qwerty keyboard at all?
I did this myself, and it really got things moving at a better rate. Right down to note selection on the numerical keypad. (Understanding of course you'll still need the modwheel/controllers on occasion.)
By the way, how's the score editor in cubase these days? Last time i looked, (Cubase 5) it was completely horrible!
Finally, i'm rather old fashioned with inputting, preferring a predominately manual approach, so take it with a pinch of salt, as i tend to worry over every note!
(Comes of not wanting to waste valuable parchment when i was a student.)
Good Luck,
Alex.