Hi and welcome to Talkbass.
Your choice of notes in a song is going to depend on many factors: the style of music...what the other instruments in the band are playing...etc...
Learning theory is going to greatly help you. Learn about intervals, chords, scales, modes, etc...Listen to basslines on your CDs. Figure out why the bassist chose what note he is playing. This is where theory can help with analyzing a tune.
For example, I see in your profile you like Flea from RHCP. Take the song "Under the Bridge": He's just playing the low note E throughout the verse, right? Not doing much at all. But then gets busier in the Chorus using more notes and also using rests. Why does he do that?
It depends on the context. So I think in your situation analyzing tunes and learning theory will help you. Have patience, it will come to you...
Edit: Hah dlloyd we posted at the same time. 