That is most definitely not a silly question!
I don’t have any Qantas bookings coming up personally, so I can’t go into my account and provide you with screenshots and I’m going from memory of past bookings. Another caveat: I’ve only ever used Qantas points to upgrade domestic bookings so if you’re talking about international, then things may be a bit different.
But … the short answer is yes, you can use points to upgrade one leg of a flight only. I have done this myself (with domestic bookings).
From memory… log in to the Qantas website and click on “manage booking”. Somewhere along the line for each flight, there will be an “upgrade” or “use points to upgrade” option. Click on it and go from there. You can upgrade whatever flight you want within each booking (eg. the return leg but not the outgoing leg).
Note that for domestic upgrades you’ll be informed about whether your upgrade was successful more-or-less on the spot. If there are no upgrades available, your request will still be waitlisted (I once had an upgrade request approved about 5 hours before the flight). International upgrades take longer to come through. This Point Hacks article will give you more information about all that.