On my RV6, in order to facilitate installation of the cowl and still have a good seal between the FAB snout and the cowling ram air inlet, I fastened the rubber seal (U shaped) around the inlet, with no rubber seal at the top, which is fairly flat. This was held on with a big hose clamp. The top part of the seal was actually mounted to the top of the FAB snout, sticking forward. The cowl went on and off much easier and sealed just fine. I believe the spacing between the FAB and cowl inlet was about 1/4 to 3/8 inch. Things do move around there so don't get them too close.
I have also seen where someone mounted a thick rubber hose around the FAB snout and this basically jammed up against the inlet when you installed the cowl. Not too pretty, but effective and simple.