Re: Don't use a power "ground bus" ...
The "ground bus" refers to the pre-TMCC and pre-DCS practice of tying all grounds (multiple loops, accessories, lights, etc.) to a common wire, or bus, under the layouts. Using the bus reduces the amount of wire required. While this is fine with low voltage AC power to the trains and other devices, it creates signal problems with control systems. My club (the National Capital Trackers) experienced significant issues with DCS control, and sometimes with TMCC, with our modular layouts which were always assembled in various configurations. Our track loops and accessories shared a single ground "bus" wire. The more complex the modules, the more likely were signal issues (Check Track, or blinking headlights). After considerable effort experimenting with filters, lights for resistance loads, and other components, we changed our module wiring so every track loop has its own power and ground wire pair (12g) and our signal problems are now greatly diminished. We also ensured each loop's ground rails were isolated from other loops using fiber pins in all three rails where we had crossing tracks.
MTH recommends a "star" wiring pattern which is all power and ground pairs that supply the track power radiate from a common point.
The star wiring is not practical for a modular layout so we have 12g power and ground wire pairs running under the modules with a track feed every 4ft. This works well for a 100 ft long modular layout (see us at York this month!).
Re: Earth ground:
The next issue you may encounter is TMCC signal reception loss where tracks pass over each other or tracks are very close in yards. TMCC signal reception in the locomotives depends on difference in signal strength detected between the broadcast antenna (the track ground rails) and Earth ground. When the radiated signal from the track overwhelms, or swamps, the Earth ground, then TMCC is lost and the engine's headlight flickers. This happens in metal bridges where metal ties or track screws connect the bridge to the rails, under overpasses where the signal from the track above swamps the lower track, and in yards, turntable yards, and other areas where track density is high.
To reduce the possibility of TMCC signal issues, start with a good Earth ground connection at your sub-panel which means the "ground" pin of your electrical outlets has good connectivity to Earth ground (your electrician can advise you here). The ground pin on the Lionel power bricks connects Earth ground to the Legacy radio components for signal broadcast. Next, connect the Legacy base to the track grounds which are connected together at a single point at the power bricks. Connecting grounds at a single point reduces DCS signal issues, but it can't hurt for TMCC either. Do NOT connect accessory and light grounds to the track grounds that broadcast the TMCC signal or each metal accessory, signal tower, or light tower and can potentially swamp the TMCC signal adjacent to the accessory.
If TMCC signal problems exist after proper wiring, start with a multimeter and determine if the track ground rails have connectivity with metal bridges or accessories next to, or above, the track. Isolate the metal accessories from the track. Next, provide Earth ground in problem areas by running a wire or foil tape above, under, or next to the track, and connecting that wire to the ground pin at the outlet, or pin 5 of the Legacy Base's serial output. There is a bit of creativity needed to determine the best approach to running the Earth ground around the layout and there are a lot of posts in the TMCC forum on this subject. In addition to the relevant OGR forum threads, check out Dale Manquen's website for his TMCC signal discussion and his pin 5 breakout connector. Always verify that your Earth ground wiring is isolated from the track power ground after any work on your layout.
Since you are building a multi-level layout where signal swamping of the lower level is likely, I recommend aluminum foil tape (a variant of duct tape) adhered to the underside of upper levels or run an Earth ground wire stapled to the underside - easy to do at layout construction, a PITA after the layout is built.
Re: number of circuits ...
One circuit for the lower level and one for the upper level would be nice. The breaker may be 15A or 20A on each, and provide enough outlets to handle the number of plugs and power bricks you add up. Don't know what code says about a large number of fixed outlets on a single circuit, but you can build a multi-outlet box to plug into a single wall outlet if the permanent outlet count is restricted. Other wall wiring and lights should be on other circuits.
John