One of the beauties of playing instruments that are not locked in like a piano is the ability to PLAY IN REAL TUNE. The well tempered scale is a CURSE to anyone with trained ears. It reduces every key to "almost" in tune.
Here is the formula for "well tempered": f(N) = 27.5*2^(N/12)
Our ears generally work differently. Chords sound "in tune" when there are a minimum of beats compared to the other frequencies being played.
here is a great link with examples:
Scales: Just vs Equal Temperament
The bottom line is that the tuner is only of any use to tune the instrument at the beginning to get a common denominator between players. After that it needs to be TURNED off. Even if everybody in the band plays to the tuner, it will sound out of tune!
To practice intonation, I recommend drones. Get your computer or keyboard to hold out a low note. Then you play a scale with long tones over that one note. The brain already has a decent mechanism to gravitate to the most harmonically compatible version if we don't overload it.
Chris Leuba (retired horn from the Chicago Symphony Orchestra) wrote an EXCELLENT book on intonation "Study In Musical Intonation". It is THE book to have for all teachers and interested players.