We trench around here and generally set the valves where the zones are. I suppose we do "mini-manifolds" and generally try and do 2-3 valves together. It is easier to do several together to keep from digging so many valve cuts off the main, and quicker for wire splices manually testing etc. The valves are generally near the zones they control.
As far as larger manifolds, honestly any ease of service savings is negated by the work needed if one of the tee's starts leaking. The manifolds I find are piped so close together that many times we end up replacing the entire manifold due to a simple pvc leak. One national contractor around here does 2 valves in each 6" box and we have to replace 2 valves everytime a pvc leak develops at the pvc fittings.
When we pipe the valves in a mini manifold we leave adequate clearance for changouts. So our manifolds are more spread out then some of the others I have seen. We put them in seperate 6" boxes.
I will say if we were able to pull poly, I would do manifolds as I think they would be more appropriate for pulling.