I've seen people routing them in front of the exhaust manifold and down, but I was thinking of routing it down the hole where the resonator was and having the filter there right inside the fender. Keep in mind, I'll be adding an AEM air bypass valve somewhere in the line.

dat is best!

isnt the resonator on the exhaust? The actual "best way" is a bunch of complicated math equations (i posted about this before), and with an ST you really wont get much power gains.
but just do what you want, obviously keep it away from heat, and still be carefull where it ends up lol even with the bypass.
Heres what i did with mine It runs up basically to the turn signal (with the invader kit, there is a big hole under the turn so i figure it must be "ramming" air in? idk it looks cool lol

Sorry bad pic, but it continues down there

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That hole you're referring to is the one I'm talking about. The stock intake box had a resonator. That weird looking random box behind your turn signal on the LH side.

here is what i did, to draw more cold air in i took and ran hosing throught the old air box hole and down into the fender right under the turn signal with a velocity stack there. you can see the hose running right under the fuze box.

wow thats pretty cool lol. is your strut bar, turned? was it too high? mine is and i had to cut out of my old hood, but mt new CF hood i dont want to cut out of, do most bars turn like that?

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Do you feel any difference?

from the cai or the strut bar, because now the bar is flat, i had to do some mods, but i had no hood clearance problemes. in the heat the hose feels like it helps.

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I've actually had mine routed both ways. Currently I have it routed under the fuse box into the fender. Originally I had it come out around the block behind the rad in front of the header and then down. My filter actually rested on the plastic piece under the car. I'll tell you I didn't really notice a difference between that and when I routed it inside the fender. I changed it due to fear of sucking in water and even though i've got it in the fender I still put a bypass valve on it. I'd recommend putting it in fender, its safer and you won't really gain anything from routing where the header is. That "resonator" for the intake was a pain to get out though. For me anyway....

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Yeah it was a pain for me too. If I had taken off the fender, it would've been easier... but I didn't wanna do that lol.