I don't use all of the dog holes but do tend to use quite a few of them at the left-hand end when using a hold-fast. I do find that having such a grid of holes is advantageous as I also use Bench Cookies with risers. The risers fit in a 3/4" hole and having the flexibility of so many hole is great.
Here are a few pictures of the bench dog layout from the lefthand end of the bench.
|Alternate vice station in the end. The right hand end|
has a similar arrangement
Chris Schwarz advocates having 2 rows of judiciously positioned dog holes from his research into the Roubo benches. The centring depends on the reach of the holdfast that you have. Have a look at his blog here