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.

Greetings,
Eraldo