It really doesn't matter if the cotton is touching the bottom of the juice channel because once the deck is screwed onto the chimney the bottom of the channel acts as the base of the tank with the full tank of juice resting on it. Providing you've dammed the cotton holes properly it shouldn't leak. Then it's a matter of using the right amount of cotton to allow the juice to flow just right.
With dual 3mm coils I find the cotton tails on either side need to be thinned out a little by giving them a brush with my pointy tweezers so as not to choke the wick holes. I also make sure I brush the cotton from underneath and all the way around to loosen the fibres so it's easier to spread it evenly around. Then push it through the hole being careful to make sure the cotton is touching the side all the way around so you properly dam the hole up so juice can't leak past the cotton and into the airflow slits. On my second attempt I didn't brush and thin the cotton tails enough so had to cram the cotton in and I choked it too much so the juice didn't wick well enough.
I think I've cracked it now so it's vaping absolutely beautifully.