You can do this as long as your computer has a stereo line input. Many laptops no longer have stereo audio inputs, only a mono mini-plug for a web microphone. However, almost all desktop computers DO have a stereo line-in. If you have a laptop that doesn't have stereo inputs, the following description will also work with external PCMCIA, USB, or Firewire stereo audio cards. Assuming you have a stereo input available, for sake of example assume we want to record two guitars:

1. Plug Guitar 1 into Channel 1 of your external mixer (via direct, direct box, stompbox, amp emulator, mic, whatever). Plug Guitar 2 into Channel 2.
2. With most mixers, it doesn't matter what channels you use, but some mixers have special use on some channels. For instance, you can find 16 channel mixers which have 12 sliders-- 8 mono channels (one input per channel), and then 4 stereo channels (two inputs per channel). In that case, it is probably simpler to use 2 of the mono channels, which gives you independent EQ and gain adjustment for each guitar.
3. Pan the guitar 1 mixer channel hard left. Pan the guitar 2 mixer channel hard right. Just to be picky, if your mixer has special mono buttons or whatever in the master section, make sure such buttons are turned OFF.
4. In the Options | Preferences | Audio Settings dialog -- the item 'Input Channel for Mono Tracks'-- Rather than Left or Right, set this item for 'L+R (2 Tracks)'
5. In the Tracks window, choose the track you want for Guitar 1. Click the track icon, and set this track to be a Mono Audio Track. Click the 'Track Number' box of the track to highlight it RED, which arms this track for recording. For example, lets say you picked Track 5.
6. Now when you record, then Keep Take, Guitar 1 will be on Track 5. If Track 6 was empty, Guitar 2 will be on Track 6. If Track 6 was not empty, PowerTracks will search up the track numbers and place Guitar 2 on the first blank track it finds.
7. Alternately, if you made Track 5 a Stereo Audio Track, PowerTracks would have recorded Guitar 1 to the left channel of Track 5, and recorded Guitar 2 to the right channel of Track 5. There are cases where this is better, but you usually get more control with two MONO tracks.
8. Once you have the Guitars on Tracks 5 and 6, you can insert different FX on each track, EQ, Echo, Chorus, whatever. You can pan each track to taste, and adjust the relative balance with the Track 5 & 6 level sliders. Often a good stereo spread might be '10 o'clock and 2 o'clock'. You can hear a spread in your livingroom or headphones, but if you are driving in your truck, you can still hear Guitar 2 a little bit, even though it's difficult for the driver to hear much out of the passenger-side right speaker. With more drastic stereo spread, some conditions such as vehicles or wide-spread stage PA speakers, you might not hear both guitars clearly.