The way I did it was to mount the scoop inlet to the fuselage so that the cowl separates at the firewall plane, leaving the scoop attached to the fuselage. This considerably reduces the bulk of the lower cowl (much easier to take on and off), and having the scoop attached cures the fuselage leakage problem.
Actually, I made the entire fuselage panel between the gear legs and aft of the rear seat, including the premanently bonded scoop detachable. I would suggest that you consider this option because working in the 'hell-hole' behind the rear seat and/or gear leg attach fittings is almost impossible without some way to access this area that is better than through the dinky hole in the rear seat. Rutan says not to do this because this is a structural part of the fuselage, so you have to seriously tie the fuselage hatch/scoop to the longerons with proper attach bolts, etc. After 24 yrs of operation I've never regretted doing it this way.