I will be running both conventional and command control, and it isn't difficult (took me some time to figure it out). Conventional control relies on varying the power to the track, whereas command control the power on the track is constant (~18v), so you can't run a conventional engine on the same track as a legacy engine.
That said, it isn't any different than conventional block wiring. If you have two loops and you have two transformers or a dual transformer like a KW, ZW, MTH Z4000, etc, what you do is isolate the loops (fiber pins to isolate the third rail in one loop from another.
So if you have two loops, let's call them A and B, connected by switches, you would:
1)Put a fiber pin between the two loops where connected by a switch, so on the 'turning' side of the switch going to the other loop, put a fiber pin in the middle rail of that turn leg. Do this for each of the switches that connect the two loops (to make this simple, envision a layout with two ovals of tracks one within the other, with switches connecting them).
2)To wire it where either engine could run on either loop, the easiest thing is for each loop, you have a double pole switch (will have three contacts on the bottom), where the outer (input) legs are each the output from transformer 1 and transformer 2, or Handle A and Handle B of a dual transformer. The center terminal goes to the middle rail of loop A or Loop B. By doing this, the selector switch allows which power source/transformer Handle goes to that loop. This gives flexibility, you could wire the handles or the transformers to each loop directly, so transformer A/Handle A handles loop A, Transformer B/Handle B, but it is better to be flexible I think.
3)For legacy, you just connect the legacy connection to the ground rail of the track (in theory you need just one, since the ground side of the track is not isolated).
4)If running legacy on loop A, you would turn the transformer/handle for A to 18v (and if using a selector switch, setting the selector switch so A power source is on loop A) . At that point, you just control the legacy engine the way you normally would. On loop B, controlled by handle B/transformer B, you run the conventional engine the way you always have, adjust the handle B/transformer B to the voltage you want.
You do have an option if you want to be able to control your conventional engine from the legacy remote. There is something called a legacy powermaster, in the scenario I gave above, the powermaster is between the power output of the transformer/handle and the middle rail for the loop involved. In that scenario, the handle voltage is set to 18v, and with the legacy controller you address the legacy powermaster (as if it is an engine), and the legacy controller allows the powermaster to change the voltage to the track, giving you speed control (and I believe whistle and bell functions, too, though not sure about that). If you put a legacy powermaster on both the A and B power output (each would need its own powermaster), you gain flexibility that you could for example run conventional engines on both loops using the legacy controller, rather than the handle.