How do you mark lawn sprinkler heads so that you don't hit them and break them with your mower when you're mowing?
I prefer to mark the heads by first trimming an area around them with a string trimmer or something similar. You may be already using this method to mark the heads that are on the edges of your lawn (spraying inward).
Other alternatives? If you want something at least as fail-safe, there are some chalk-like (temporary) grass-safe paints. (I know that Krylon has such a line.) You can also use flags or small cones. Over time, however, these alternatives seem to add an extra step--one too easy to skip in haste.
There are some permanent marker options to consider, depending on how intensively you care for your lawn and whether or not you care for the result. Google key words "sprinkler head protector" for a selection of devices that you can place over/around the problem heads.