A pure 2QB league with 12 teams is rough as there are only 32 starting QBs on any given Sunday and there's going to be demand for 36 QBs on rosters.
IMO for a 2QB league you need 10 teams or fewer.
An OP Flex (any offensive player - QB/RB/WR/TE) is a possibility. At least in that situation the teams that don't have a third QB for bye weeks can start someone in that roster spot.
In the case of an OP spot, some GMs may carry a handcuff QB (Nick Foles for Mike Vick or Brock Osweiller for Peyton Manning, for example) but most GMs will prefer to carry 3 QBs. The dynasty league I'm in uses an OP slot and every starting QB in the NFL is owned, as well as a few backups. If you don't bench a handcuff, your roster is in bad shape if one of your QBs goes down.
With 6pt pass TDs, the value of QBs in the league skyrockets when you double up on the position.