When the coil split is not currently engaged the HB will run and sound just as it normally would. When the coil split is engaged one of the coils is send to ground, read turned off.
So no worries!
When wired correctly all should be well. Donīt know if you wanne go for an autosplit (one position on the switch being normal, the neck is split NB with middle, etc.) or if you want a push pull poti, but if either is done correct you will still have the normal NB at your disposal as a standard option.