I'm sure you can. I had a set of k&n's on a arctic cat 800 mtn cat. I put the stock box back because the powder would plug them up. I didn't have the prefilters on them though.
I don't believe any under hood air is good. Moisture can make slides freeze and warm air just robs horse power. The best thing is a snorkel thru the left side speedo hole.
SLP also makes a cold air intake with an airbox top and an aluminum plate with about 7 1-1/2 inch holes in it to pull from the top of the hood between the steering post and the gauges. That has worked well for me with no bogging.
i run filterpods with prefilters and havent had a problem with them, key is good ventilation. i never noticed any horsepower drop and my EGTs stayed the same when even after i switched to pods. plus they are lighter and more room to work on stuff.