So, to review,
1) The audio in jack on the Mac is NOT a pre-amp at all, so you need to pre-amp the signal to get a decent tone.
2) This pre-amp could come from built in active electronic pickups, your amps preamp stage, or a 3rd party preamp device.
3) When using an amps preamp section, you want to go instrument into amp, and use the LINE OUT jack from the amp to your computer. NOT the speaker out. The speaker out has already passed through the power amp section, and would be way to powerful for your computer... maybe even damaging.
4) Apple basically lied when they said you could just plug in and go with garageband.. you can, but the tone will suck!
5) Once all the above has been done, you must adjust the settings on your computer (appropriate input in the system prefs, etc) as mentioned above.
Record away!
I learned most of this the hard way a year ago too. Have fun,
James