One very good practice for this issue is to tune your bass by ear, using the harmonics and a tuning fork.
You start by tuning the D string (if you have no tuning fork, use your tuner to tune the D string). The harmonic located above the 7th (or 19th) fret is an A (220 Hz) that you can compare and match to the A (440 Hz) of your tuning fork that you hold (vibrating) above your pickup.
Once your D string is tuned, you can tune the G string by matching the D harmonics respectively located above the 7th fret of the G string and 5th fret of the D string. Listen to them carefully. Play the D string (you reference) first, and then the G string, trying to detect whether your G string is flat or sharp. The thing you should pay attention to are the beats (periodic intensity modulation) that can be heard when the tuning is not perfect. The frequency of the beats is equal to the difference of the frequencies of the harmonics of the G and D strings. So, if you hear a 2 Hz beat (2 beats/second), this means that your G string is 2 Hz too low or too high. You need to adjust it so that the beat becomes so slow that it is no longer noticeable.
You can thus proceed by tuning the A string (5th fret harmonic on A string matched to 7th fret harmonic on D string), and then The E string (5th fret harmonic on E string matched to the 7th fret harmonic on A string).
Then the frequencies of successive strings are exactly in 3/4 ratios, i.e., a pecfect 4th apart.
The method is more accurate for the high strings than the low ones, but that is fine, as our pitch discrimination is also more accurate for high sounds than for low ones. For a similar reason, even with a tuner, I find it more accurate to tune by using the octave harmonic (12th fret) rather than the open string.