To answer my own query. I wasn't able to check for Aer Lingus but BA offer the option to add stopovers in London easily on their website. Booking as a stopover OR 2 separate bookings using Avios was the same cost (when only using BA). However if you booked AA for the second segment it worked more expensive for the cash portion with 2 separate bookings versus 1 booking with a stopover.
So maybe if the OP prices up the flights and availability he wants with 2xOne-way with Aer Lingus and calls BA or Avios(if you can??) to price up the flights as a stopover and see what's best. But the easiest option without hassle is probably 2xOne way flights.

All examples are business class flights:

2x One-way
CDG-LHR BA J 15k Avios + €0.5 9Nov
LHR-JFK BA J 80k Avios + €175 11Nov
or LHR - JFK J 62k Avios + €836 11 Nov

Stop Over:
CDG-LHR 9 Nov BA J + LHR-JFK 11 Nov BA J} 95k Avios + €175
or CDG-LHR 9 Nov BA J + LHR-JFK 11 Nov AA J} 77k Avios + €621