I will try scram out later tonight when the kiddos are in bed as I would like to start my build in a day or two.
Had I known you had RR-Track, I wouldn't have recommended SCARM, though I do use both. I generally work in RR-Track because I find it quicker and easier to get things done, then convert to SCARM, mostly to see its 3D view and for Mixy's simulation feature when it gets released. The more I use SCARM though, the easier it is for me to get things done. My main gripe is having to select a track and then select a menu option to move things vs just the left-click in RR-Track. It is nice though to be able to just hit the spacebar to repeat the last track.
I just noticed you are using the RR-Track Lite that came with your set, so you are limited on track libraries. I started with Lite too, but quickly decided RealTrax was not for me in the long run and I purchased the full version with additional track libraries. That was before SCARM was released. If nothing else, SCARM will give you the option to see what you can design using other track libraries, like Atlas, GarGraves, FasTrack, etc. IMHO, SCARM is worth learning just for the 3D view, though I've gotten better at 3D design in RR-Track. At any rate, it's free for now and another option. All track is not created equal, so you can't just swap brands of track and get the same results. Plus, you might find that O31/O36/O48/O60 FasTrack gives you more options than O31/O42/O54 RealTrax before you get too heavily invested in RealTrax to make the switch.
I also haven't had any serious problems with RealTrax and mine has been taken apart and reconfigured many times. I just think it's too noisy and I'm not a big fan of plastic roadbed on a more permanent layout unless the layout is going to be covered with something like indoor/outdoor carpet. I haven't had any experience with FasTrack, so I don't know if I'd like it any better. For sure, there are more options with FasTrack, so it's something to consider if one is going to use track with plastic roadbed. I don't know how long you've had your set, so you might not have enough experience with it yet. I may use the RealTrax I have on my top level though since it's independent of the bottom level and will be using O31 curves. If nothing else, I'll use it temporarily.
Anyway, plan 1 lets you run 2 trains at the same time without intervention. It does have tighter turns, so that limits the equipment you can buy, but I don't think O42 increases the options all that much. Plan 2 lets you run 3 trains, but you have to manage the single main line to avoid conflicts. And if you really want to avoid accidents, you need to do some creative wiring to stop trains if the main is already being used by another train. Plan 2 is definitely more of a "working" plan that will require the operator to pay attention to what's going on or there will be some crashes. I think I would consider eliminating the passing siding at the bottom in order to separate the inner loop, kind of a combination of the 2 plans.