If you have a stereo mic input, you still need a way of getting both mics you are using to separate channels. There exists an adapter called a "stereo to mono splitter" that splits the stereo input jack into two mono jacks, routing the signals the right way from each mic. Don't fall for the so-called "stereo mics" because the separation between mic elements is not sufficient to get good stereo imaging. Definitely go with two separate mics. Are you using high quality mics for recording? If not, stereo is just going to make your recordings sound twice as bad...
The alternative is to install a higher end USB sound card from someone like M-Audio or Creative Labs. I believe the adapter would be cheaper to try first. There are also small USB control surfaces/mixers out there which will give you access to more channels, but I've never had a chance to play with one yet in Linux. (I'd love to know about a unit like this from M-Audio, Tascam, or somebody like that.)
Y'know, this presumes you are doing live recording? If you are working with separate tracks "studio style", record everything mono, then pan your tracks to create the stereo imaging you want. You can even duplicate tracks and manipulate them to create stereo ambience.
@Just18: I use Audacity a lot, and don't find it at all complicated. Try Ardour for something truly monstrous. (I'm glad I know one of the developers for Ardour - I pick his brain all the time for stuff when I use it, otherwise I'd be lost most of the time.)