Hello.
I have CB6, and have used it a lot with VE Pro with Vienna Instrument Pro. I setup VE Pro with instruments loaded, each on its own MIDI Channel.
In CB I choose VE Pro in the VST Instruments window, then add as many MIDI tracks as I have instruments in VE Pro, and select then select VE Pro MIDI channels for each VE Pro instrument. This way, I only have the MIDI tracks and one Folder showing VE Pro, and all the MIDI channel tracks.
I also have PT9, but haven't used it for a while. I think I'll give it another try, since you have such good experience with it.