I am having a similar problem as Marcelo... However, in order to keep the agenda flat I only want the parent PROJECT headline (the inner most) to be the prefix. In his example this would be the following:
My-sub-sub-project NEXT Call Liz RE: account creation :@call:@work:
The problem is that I did not yet find out how I can get the <parent project headline> (in this case: my-sub-sub-project) as agenda prefix.
Until this is solved I rewrite the project name for all todo-headlines in the project.