Finding the right notes on your bass can be challenging when you are in the middle of playing a song. One way to get better at it, is by understanding the system behind the fretboard before you play the song.
Correct instrument tuning is very important. Tuning your bass should always be the first thing you do whenever you play. A tuned bass just sounds so much better.
What ever you do, do not use overtones, harmonics, flageolettes (or whatever you want to call them) to tune your bass guitar. I have recently been warned against using harmonics while tuning an instrument and am warning you now.
Use a tuner or the fifth fret method instead. It's that simple.
ToFret offers a visualisation tool for the fretboard of stringed instruments. Currently it is able to show all locations of any note on the neck of a bass guitar.
Do you use bass tablature? If you do, toFret offers a bass tab to fretboard converter. It will show you the actual position of the notes on the neck of your bass guitar. You can play the tab, not to get sound, but to see the notes and patterns being played in sequence on the fretboard.