I follow the opinion of throw the filter on the tb, but if you wanna keep your pretty blue pipe, go to Home Depot or Lowes and buy a 3" to 3" coupler and put that on the throttle body, pipe on the other end, filter on the end of the pipe.

I think either way though, you're not going to see any feelable difference, you might get some better sound by removing that baffled part... that's the part that's restrictive and makes turbulence in the air.