In case anyone is interested in the outcome:

Yes it can be done, with the correct miles deducted (one way F, one way J). Do note that for mixed class bookings though, the system has a knack to price it as two trips. For my case I was first quoted the rate for a one way j class MNL-SIN and one way f class SIN-SFO. It is possible to charge the highest class flown fare though, so ticketed as a one way f class MNL-SFO. The agent I spoke to didn't know about this and I had to insist on speaking to a supervisor.

The system can recognize it as a round trip, so I could avail of the free stopover on the way back in SIN.

The multi city button for redemptions on the website is gone, but after selecting your desired flights, there will be a pop up asking if you wish to make a stopover. If you do you choose the date for the segment after stopping over and choose your flight as again. Apparently sq thinks it's more intuitive...