I haven't actually replaced them on mine, but I do have the engine (I assume you mean the "new era" 2006 or later J, not the awful one from the 1980s and 90s). The tires are on the 3rd driver, which is not pinned to the rods. So, like the Kato Mikado, you should be able to just unscrew the cover plate and remove it, then carefully lift the 3rd driver axle out. Slip a new tire on (use something smooth, like a toothpick, to guide the rubber tire around the rim as you slip it on). Then replace the driver and screw the cover plate back on.
Since the 3rd driver isn't pinned to the rods, you can't mess up the quartering. You might get the driver in oriented a little off, so the counterweights or the crank hole area don't line up with the rods, but that will not affect the running. If you can see that it doesn't look right, just gently lift it out, rotate it a little and drop it back in.