Simply open or close the hierachy of bookmarksto look exactly as you want to see it when the pdf opens and then save the file. When you open it up in reader, it displays the bookmarks as they were at the time of your last save.
This allows you to decide on a bookmark by boomark level what is open and what remains closed.
This also allows you to open the 1st and say 4th bookmark to show all 3 tiers, the 2nd bookmark to show no tiers, and the last two bookmarks to show only the first and second tiers. Endless combinations. It isn't all or nothing.
Hope that is helpful. Terri