You can get a midi converter for pretty cheap. I use an M-audio that I got for ~$50 at Best Buy 5 years or more ago. This will allow you to record what you play on your guitar. Once it's in digital format you can manipulate it any way you like. I do not use "layering" in my music, it's mostly single guitar and when I use multiple instruments each is live, not sampled or digitally created.
I am not quite sure if the free distribution of the pro tools software has multiple instruments but I know it has effects. Other instruments is a small leap so it's gotta be out there.
My point is, you can record your guitar playing in digital format, copy and paste into other tracks and change the sound for that track. If you know what you want to play you can play each layer and edit the sound after the fact. If you know your music notation and theory (which you post implies you do not) you could copy multiple layers of the same track and change notes via computer manipulation to create harmony.
I'd recommend looking up pro tools and M-audio as a start. These are not the only tools of this type, just the ones I'm familiar with.