On my America I am running a K&N replacement for the stock filter inside the stock airbox.
http://newspeedmaster.com/html/k_and_n_air_filter.html
I run with the snorkel removed,but when I wash the bike I pop it back on with a plastic bag over it to stop any water getting in there.
Further gains can be had by fitting a bellmouth in lieu of the snorkel and also drilling a hole in the bottom of the airbox.This hole should be no bigger than the size and shape of the inside of the filter.(If you ride in rain with the hole in the bottom,you will get water into the system.)
If you wish to fit K&Ns directly to the carb/throttle bodies,you will need to entirely remove the airbox,and from memory,I think this will require battery support mods and a carb brace.
http://newspeedmaster.com/html/airbox_removal_kit.html
Dont forget,whichever way you go,you will need to rejet/map,1,to reap the benefits of the mods and2,to protect your engine.
The benefits of the total removal of the box is supposedly bigger hp gains but I cannot verify this personaly.
The benefit of the way I have mine done is, it is totally reversible to stock in 5 minutes,but I still get most of the gains.Remember,if you are sucking warmer air into your motor,you will outweigh any gains of more volume,so bear in mind where you suck that air from.