Learn your scales and internalize the intervals. For me It's helped tremendously to think in terms of scale degress and intervals rather than Note names.
Major and Minor pentatonic scales were life savers for me, as well as learning how to arpegiate minor and major chords...
Within the context of the major scale. Say for instance a song is in the key of C:
C = 1, d = 2 , e=3, F = 4, G = 5, a = 6, b = 7
Once you learn the Major and Minor pentatonic shapes. The Capital lettered notes above are Major, and the lowercase a minor.
Use the appropriate scale when the songs progression moves to that particular chord.
check these out:
http://www.youtube.com/Torch7 http://www.youtube.com/gospelbasslines
Hope these help. If not IM me, and ask questions where things aren't clear.
What sort of church do you attend, what type of music is being played? Maybe I can help you further if you share those details with me.