For what it's worth I have 2 miditracks per VSI instance. These all go into one folder per section with the '2nd' set going into a second folder within the first. eg - 'Strings Folder' - Violin 1, Violin 2, Viola, Celli and Bass. Then a 'Strings Folder CCs' -Violin 1 CCs, Violin 2 CCs, Viola CCs, Celli CCs and Bass CCs within the 'Strings Folder'.
These folders can be opened and closed as required either together or separately and avoids a cluttered track list.
Any switches or controller info that I record on the first Violin 1 track gets transferred to the Violin 1 CCs track. I can then add additional switches and controller information as required.
This helps me in several ways. When the Violin 1 track goes for copying for playing by a live orchestra you don't have any switch notes, articulation key switches, or controller information creeping into the written score-parts.
Another way I find this method useful is I find it easier to then edit the controller information (such as volume or velocity X-fade on a slider) and/or key switch information without the risk of disturbing the actual 'part'.
I don't say this will work for everyone - or anyone - but it is the best way I have found to date. [*-)]
On another topic - I have seen other threads where folks are overwhelmed by the size of this library. I too sat and looked at it for a while [:D]
I have found that saving your own 'basic' set up and then adding matrix and patches to this 'basic' set up lets you grow into this library while making your growing set up backward compatible.
Good luck - and don't panic [:D]