Well I use Logic and while I don\'t have GPO yet I may have some useful tips:
In the environment, I ussually create a multi-channel midi object and route it to the audio instrument which contains kontakt. This way you can create different tracks for each channel in the arrange. I don\'t know if Kompakt can do this but I would be surprised if it can\'t!
You can setup different folders with different sections of the orchestra if you want. When I\'m using GPO along side a bigger audio project I like to keep all of GPO grouped together and in orginaized sub-folders - because I don\'t need to be looking at all the individual tracks at once and this also makes it easier to loop or cut-and-paste groups of the orchestra and still be able to edit the individual instruments.
For mod wheel and sustain info, yes you can do all that stuff in the hyper editor. I have a small midi controller (a 200 dollar one!) with knobs on it that I like to program so they control different perameters within Logic or a spacific instrument (be it VST or otherwise). If I want to get all fancy I could set it up so each knob controls the level of an individual channel, or even changes the velocity or modulation. I guess it\'s personal prefference, I tend to mix better with I\'m not looking at a screen and have the ability to close my eyes and turn knobs. But anyways, yeah you can edit everything manually and be just fine.