I'd like to outline how we go about setting up the instruments. I welcome input from others.
I always start with the truss-rod, then nut, then bridge.
We measure truss-rod relief on the outside bass string (B-string on a 5 or 6, E on a 4) by fretting at both the 1st and 17th frets, then checking the gap between the string and the 7th fret.
For players with a light touch .020" or less of relief is about right. That's about the thickness of a Dunlop .5 mm guitar pick. Players with a heavier touch need to loosen their truss-rods for more relief.
Ideally you want the neck as straight as possible. You'll know if the neck is too straight if you are getting excessive buzzing in frets 1 through 7. A little buzz when you dig-in is OK and to be expected. You just don't want to have buzz happening when you are playing normally.
Once the neck is adjusted correctly, double-check the nut. Open strings should not buzz. When fretting at the 2nd fret, there should be a slight gap over the 1st fret - not more than the thickness of a piece of paper or two. If you are getting buzzing on the open strings you can either loosen the truss-rod 1/8 turn or have the nut replaced (they wear out and need replacing from time to time).
Only after checking the nut and truss-rod do you go to the bridge. At this point if you want to lower your action further, you can lower the saddle riser screws. It's best to do this in measured amounts. I.E. 1/4 turn on every screw, re-tune and play for a bit.
You can lower the saddles until you get buzzing in the upper frets 10th and up. The harder you play, the higher the saddles need to be. The lighter you play, the lower they can go. It's best to keep the saddles as low as possible (without buzzing) as higher saddles create more stress on the string leading to breakage.
The easiest way to check intonation is to tune the open string, then compare the pitch of the 12th fret harmonic to the fretted 12th fret note. They should be the same. If the fretted note is sharper than the harmonic, the distance between the 12th fret and saddle is too short and the saddle needs to be moved back a bit. If the fretted note is flatter than the harmonic, you need to move the saddle forward a bit.
Once the saddle is moved, you'll need to re-tune before checking.
If you use Dingwall strings and maintain your truss-rod adjustment, you can go years without having to touch your bridge.