When Graeme says the copilot side needs to be in FMS2 he means as a navigation source, as shown on the left hand side of the PFD.
It’s part of the navigation database. If you select an ILS (or LOC, I think) approach in the DEP/ARR page then it will know the frequencies to auto-tune when the time comes.
This seems plausible. Unlike a Boeing or an Airbus, the Challenger will do a fixed 3° angle descent path (by default, it is overridable on a per leg basis), not an idle thrust descent. As such if you’ve manually put altitude constraints on the descent I’m not surprised they’re not exactly on the 3° path, as such the aircraft plans multiple step-downs and shows a TOD for each. There’s no need to “help” it along, it’s capable of VNAV descents all the way to the threshold. Include a screenshot of this situation if you’d like to learn more.
It’s actually the opposite, if I am understanding the query correctly. Without VNAV the plane will descend to the altitude you’ve selected via the flight control panel (blue) regardless of what’s in the flight plan. With a VNAV-enabled vertical mode, even if the altitude you’ve selected is lower than what’s in the flight plan the plane will not descend past any constraints (magenta).
So the throttle icons (“ghost throttle”) came up but when you move your throttle levers (what hardware?) there was no change on the overlay? That’s quite odd. The overlay should show you the position of your hardware levers when they are desynced from the virtual cockpit levers. You’re 100% sure you weren’t accidentally in reverse thrust mode as far as X-Plane was concerned? This is where a video would help also, but I’m linking to another post just for more of a description of the “ghost throttles”.