You said 12VAC, so there's no positive or negative.
Connecting power supplies in parallel is generally not recommended, because it can cause issues with one power supply trying to inject power into the other. If they are two identical wall warts with an AC output, it should be possible to connect them in parallel, but they must be in phase, otherwise it will result in smoke. Connect one side together and measure the voltage between the other connections. It should read close to zero. If it's double the voltage, then reverse the connections to one of them and try again. Once the voltage is close to zero, the other sides can be connected together.
What exactly are you powering? Please post some schematics and/or provide links to datasheets and/or the place where you bought the equipment from.