I'll share my limited but recent experience:

Waitlisted 2x Suites Saver on April 9th for the SQ11 (NRT-SIN) flight on April 30th. Did not choose a second option, so just had a waitlisted PNR. They didn't deduct any miles or take any payment upfront. I then made another confirmed booking for 2x First Saver on HND-SIN on the same day, which was the backup in case the waitlist didn't clear.

Called 4 times in the week prior to the flight to ask them to expedite/confirm it, including once in the morning of the day before the flight. That afternoon (roughly 30+ hours before the flight) I got an email from SQ saying that my flight was confirmed, and that I needed to confirm it online before 24 hours prior to the flight. [In the end, only 4/12 of the Suites were taken, including myself and my partner.]

Since I used my miles to book the confirmed HND-SIN ticket and didn't have enough to confirm the waitlisted one as well, I first called in to cancel the HND-SIN tickets (with a $30 USD fee) and asked them to return the miles immediately so I can book the waitlist. If you didn't make separate bookings for the waitlisted/confirmed flights then this paragraph can probably be ignored.

At this point I could have either continued on the phone and ask them to confirm the waitlist, or just log into my Krisflyer account online and complete it myself through the manage booking tab which is very straightforward. When I tried doing it myself online, I clicked manage booking on my waitlisted PNR and was given the choice to select the flights I want to confirm, with a warning that any other flights would be cancelled. This is likely the step where the confirmed flight gets dropped, which would mean it is a manual action by you the user and not an automatic action by SQ.

No idea on the 'choose a second option (must not be a waitlisted flight)' part, but hopefully it sheds some light on the confirmation/cancellation process a bit.

All the best with your waitlists!