When transcribing I try to learn the original bassline. It will help your playing style develop even though you still don't know why they are doing what they are doing. I don't tab anything down though it's too time consuming, I just download the song onto my pc, and set markers in the song by sections until I learn that phrase of the music then slowly move on until I know the whole song from memory. Then once you know the original you can add your own flavor or play it note for note (this also keeps the keyboardist off your case when you know exactly the way the bassline is played, alot of times the keyboardist is playing the root with a bunch of passing tones whereas you're supporting the melody completely).
