AFAIK, that checkmark is akin to a keyword, just like any other in iPhoto. Think of it as a way to temporarily mark some photos that you plan to work on or print? Perhaps it would make more sense if the Smart Album feature actually allowed you to select "photos whose keyword includes the checkmark." As it stands now it just allows matching text, which prevents you from using the checkmark as a delimiter.

I usually just end up creating a temporary album and dragging photos into it. The keyword implementation in iPhoto has always been half-baked IMHO. You should be able to keyword photos much quicker, by way of contextual menus or hotkeys. Otherwise the "time saver" ends up taking way too much time to actually enable.