Higher partials tend to run flat on tuba, lower partials tends to run sharp. If Eb2 is rough, I'm assuming D2 is probably rough as well, unless they're already using 3rd valve by itself for D2 (recommended for most tubas/students).

Anyway, here's the typical loadout (always tune the master/main slide first):

D/Db2/Gb2 - Set 3rd slide to Gb with tuner. Pull out 3rd slide when playing Db/D(assuming they're playing D w/ 3rd), push back to Gb position when not playing it (for low brass boy brains, bc they'll actually just leave it there sometimes).

Eb/Ab2 - Tune 1st slide to Ab. Pull out 1st slide when playing Eb/D(assuming they're playing D w/ 1&2), push back to Ab position when not playing Eb.

Tune 4th slide with C2/B1. B1 tends to run sharp on Miraphone tubas, even with the slide all the way out. This slide won't ever need to move in realtime. Y

You can fix those pesky B1 sustains by having them use the 1&2&3 Sousaphone fingering and pull out both the first AND third slides for that note, but you'll need roughly a quarter step of length (4-6 inches of pull combined).

2nd slide almost never moves for anything unless you've got a weird off-brand tuba or mouthpiece....or it's just dented up to hell.