hey Skyskinner,
I am a relative newbie myself, less than a year, you probably have a leg up on me, because you get music to look at. In our church we listen to the song and the musicians just run off and play.(well all except the newbie bass player, the prior bass player left)
You will also need to learn about modes and how the song progresses.
I recommend getting the book "Bass for dummies" it will go into this.
Also check out
http://www.cyberfretbass.com good tutorials on this.
If that doesn't help contact me and I will attempt to shed more light on the subject.