This will depend on upgrade availabilty. If there is upgrade seat availability when you "book" it, then yes it is a single 8000 point upgrade. But if you need to waitlist for one or both sectors, then it is processed as two separate upgrades and costs two lots of points. This was explained to me by QF as a necessity of the system since both upgrade waitlists are considered separately and may not be granted at the same time, and one or both sectors may not available.

I requested to upgrade FRA-SIN and SIN-MEL (two different flight numbers), and had to use 4 upgrade credits for the FRA-SIN and points for the SIN-MEL since both had to be waitlisted. So far the FRA-SIN has upgrade waitlist has come through (thanks Qantas), but the SIN-MEL upgrade is still waitlisted (fingers still crossed since as of today there are 3 seats available for paying passengers about 48 hours before departure).