During take-off, it's a good idea to highlight systems with their own color code as you take-off the items.  Accordingly, all notes pertaining to those items should also be highlighted with the same color.   An example would be:

Switchgear and Switchgear Notes	Blue
Fixtures and Fixture Notes	Green
Branch and Branch Notes	Yellow
Devices and Device Notes	Pink
LV Devices and LV Device Notes	Purple
Fire Alarm and Fire Alarm Notes	Orange

This will make association of the items taken off and all related notes easy to identify when summarizing your estimate.