How do I make a 1x1x2 piston door that opens when I step on a plate and not the other way around?
Simply put in a NOT Gate. A not gate is a redstone current running into a block which has a redstone torch attached to it (as shown in the first screenshot).
Here is a good example that uses a NOT gate.
If you already have the door working (but inverted) just connect the pressure plate to the pistons using a NOT gate (a torch on a block) to invert the signal and therefore the door.