Most airlines I know of pay only flight time (or something less like "average block" if you are at Mesa). Per diem is paid from the time you start a trip till you finish it or what is called "time away from base" this is usually abreviated TAFB. So the difference between your duty time and your flight time is the time you are making that cool buck and a half (or whatever your per diem rate is). Thats why you will hear airline pilots ***** about "sits" and schedule "efficiency" because it sucks to be at work but technically off the clock.

To answer your question specifically: you would get paid your flight pay for 5.5 hours and per diem for 7.5 hours. That means for 2 of those hours, you were making just per diem.