BOH/SOU
A sensible approach to the BOH/SOU routes would seem to be the same as BA use for London. Take a search of flights London to Amsterdam for instance, BA offer LHR, LCY and LGW, you can fly out of one and back to another. This maximises the schedule availability and sales.
Seems obvious to me that this would be the right approach for Flybe at BOH/SOU too.
FF