I think it depends on what you prefer. Some adjusters take offense if they show up with a roof chalked, they think you're trying to do their job for them. With some insurance companies and some adjusters, you do need to do their job for them. My recommendation is to not chalk the roof for the more friendly insurance companies and adjusters. Chalk every single damaged shingle if it is Allstate or AmFam (and a few others). If the adjuster doesn't like it, too bad. Here's the thing though, make sure what you chalk is really damage and not blistering or bird shit. Have the HO there and coach them to watch to see if the adjuster inspects all the damage. If he doesn't, gets down and denies the roof, have the HO raise hell. Call in for a second inspection. If it is a known unfriendly insurance company and/or adjuster, you can even ask the HO to video tape the inspection to later prove the adjuster ignored the chalked damage.