Okay, first things first, separate controllers 'always' need separate supplies. There are instances where one supply can run more than one controller, but it's unlikely anyone will ever have such an instance. Hence, your second drawing is better than the first.
You don't want to limit the current into your DC controller, so having calculated the resistance for your LEDs seemingly correctly, I would suggest running them at somewhat less than 20mA and consider a series resistor in the order of 560 ohms or more. In addition to this, aside from some very specific circumstances, every LED should have its own resistor, you're using tricolour LEDs, so I would use two, one on each cathode, because I like to be elegant and tweak brightness individually, hence you may find you use different values for different colours. The other acceptable thing may be to use one resistor connected right at the LED anode.
I would use your switches to drive a relay to switch between the track controllers, one side of the switch powering the relay, the other side of the switch deciding which LED is lit, and yes, I would power all the LEDs from their own supply (as in one supply for all the LEDs). If you don't want to go with relays, then I would suggest a four pole switch, giving the LEDs a separate set of switch contacts, isolated from your track wiring.