Hi,
Just a disclaimer - i am a neuromusculoskeletal physio, not a cardioresp physio...
But i think the theory behind the upside down usage is that to blow and hold one or two balls up (triflo incentive spirometer), then you will need to have taken a deep breath to begin with.
Some people find the inhalation difficult and so can't do even one ball up. To encourage the patients by giving them an achievment, again * i think *, you turn the spirometer upside down.
THerefore, upside down is a level lower than one ball up during inhalation.
Obviosuly, the ideal is for nice, equal, lateral basal expansion but i guess anything deeper than what they are doing is better than nothing.
I hope that helps. I haven't looked for any research to back up my claims i am afraid...just personal experience.