So in this situation, most likely, your power hits the light first, then down to the switch with 12/2, then over and back in that 12/3. My best guess is that the black wire on the switch is your HOT. The red and white are the TRAVELERS over to the other 3-way switch. The black from the 12/3, the one that's tied to the white of the 12/2, is the SWITCHLEG from the second 3-way straight to the lights. Your whites, in this case, will occasionally be HOT.
3-ways have nothing to do with the number of lights being switched on. 3-ways come into play when you have more than one switching location. 3 or more requires 4-ways between the 3-ways.