In terms of melodic lines within a piece, you can't just set the HD to just intonation in the key of the piece, it has to be relative to the chord structure at that moment in time. For instance in the key of F, if the melodic voice has an A and the harmonic structure at that moment is a I chord, they would need to play that A lowered to sound right within that structure, but if that A happened over a vi chord, it'd be the 5th and need to be slightly raised.
The reality is that these adjustments are so small that they really aren't that perceptible when things are moving around a lot. So in many cases this can be a non-issue except during sustained chords. Depending on the source you look at and the person doing the hearing, it takes a difference of somewhere between 6 and 12 cents before humans perceive a pitch difference. That variation is even greater when the two pitches have different timbres (as in we don't perceive out-of-tune as well between instruments as we do within sections). Also, the perceptible difference has been shown to be smaller in harmonic structure vs melodic structure (i.e. when listening to a melodic line things have to be more out of tune to be noticed, but it takes relatively small differences for "beats" to be perceived when two pitches are happening together). So, if you really want to get into the nuts and bolts of it, vertical intonation is going to be what the ear perceives as sounding good or not more so than linear intonation.
All that to say, do what sounds good. This is why I have my band sing A LOT. When singing, your ears will naturally make you put the pitch where it sounds "right" rather than defaulting to the mechanical pitch tendencies of an instrument. If you can get them to listen the same way, and make it sound the same to them, when they play that it does when they sing, it'll be great. Whether you are using just or tempered intonation at any given time is very much secondary to being in tune with what's happening around you.
: We are having a friendly debate related to
: using the harmony director in class. Here
: is the debate:
: -All of us agree about using just intonation
: when working with chords to make sure the
: correct chord tones. Some of our directors;
: however, play scales and melodic lines using
: the lowered third in the key while others
: say the third should only be lowered within
: chords not all the time in a key because
: sometimes the third in a key is the root of
: chord and not lowered. When melodic/scale
: material is played with the lowered third is
: does not sound right to me, especially when
: singing solfeggio to a scale.