The first picture doesn't work but the second does.
I believe the line that is nearest in the picture just plumbs to the lower portion of the airbox (pre-air filter). I would imagine that could be discarded.
The other is a vacuum line of some sort and if left disconnected will probably trigger a 'Check Engine' light and possibly cause the car to run rough or hurt your mpg. In the stock setup it is before the MAF sensor - I'm not sure whether or not it HAS to be before the MAF to work properly so you may be able to put a nipple on your intake tube after the MAF, assuming you're going to clamp the filter right on the front of the MAF.
Search these pages and Google, there have been plenty of threads on CAIs for these motors; there may be something in one that helps out.