Music/computer recording question

So I recently bought a Soundblaster Audigy to do some recording. The system comes with some built-in effects so you can make your guitar and vocals sound cool. Anyways, I laid down a 'metronome track' in a multitrack program, and I wanted to add a guitar with effects onto another track. Is there any way I can add the guitar track without having the computer process the metronome track, and without having the metronome track also show up on the track that's only supposed to be guitar? The "What U Hear" option records exactly what plays through the speakers, including instant messenger beeps, dialogue box pop-ups, and the drum track, which plays when I'm playing the guitar track. The Line-in option allows me to hear the processed guitar as I play it, but it records the unprocessed guitar.

It seems like this is so fricking obvious for Soundblaster to address, since this problem must come up for any user of multitrack software, but I can't seem to find any documentation regarding it, and I can't figure it out! Someone help!