Use Addon Linker, create folders for example per area and type where you save your addons if outside the main community folder (suggested as they are easier to handle), I have:
UK
WEST USA
CENTRAL USA
EAST USA
WEST CANADA
EAST CANADA
GLOBAL
LIBRARIES
NON SCENERY (under this I have a folder called Fixes where I put water fixes and so on)
In this way from Addon Linker you can quickly switch on and off things and test what causes issues 
you can create more sub folder so to keep your addon nicely organised.