Intonation is always a topic among hornists. One note I listen for carefully is C-sharp, third space. This should be a great note; often it is not.
The C just below this note (fourth space) should be one of your very best notes; no valve slide compromise settings are involved, and it is a good harmonic. So the first step to a great C-sharp is a great C. If you feel this C lays high on your horn, actually, it is correct; the reality is that everything else is tuned low in relationship to that note, and the horn is also tuned too high. Tune the rest of the horn to that note.
Once that C feels great, you only need to adjust ONE tuning slide to make a great C-sharp, the third valve slide on the B-flat horn. Adjust that slide so that C-sharp is perfect, so that on your tuner the needle is straight up on both pitches. No compromises should be involved.
On many horns the third valve slide on the B-flat horn will need to be pushed in all the way to achieve a great C-sharp. In fact, on my old 8D, I had the slide cut so that it was shorter than standard to produce a very comfortable C-sharp, at the suggestion of my teacher at Eastman, Verne Reynolds.