Try Audacity.com I believe it is a multitrack recording software that is free. If your recording is at low levels and you can punch them up, but depending on the amount of gain, you lose tonality and just get volume and or distortion and something known as a digital footprint. Kinda sounds like ghosts in the machine so to speak. It's probably worth your time to invest in a small 2 or 4 channel mixer to give you gain and some EQ before recording. I use a Mackie mixer for my pre-amp and it works beatifully, but there are many cheaper well made mixers out there as well. Good Luck!

Kudzuman