The actual polarity of the track feed wires changes when you reverse direction with the controller. The mark on one wire is only to assist in identification. You should be OK if you connect the common return wire to the same terminal on each controller and to the same rail (left or right). You can connect wires from the other terminal to isolated blocks of the other rail. This works as long as the controllers are powered from separate transformers. Common-return wiring is not suitable if you have a reversing loop or triangle on your layout.
You should be able to buy an analogue multimeter for £5-10.