welcome,this is a great place. One thing I recommend is trying other rail design programs like Scarm or RailModeller pro (not sure if rail modeller pro has a windows version), they have free versions and you can see if you can work with them. I had bought RR track software but I found it hard to use), I ended up being able to work with Railmodeller pro and design the layout. It makes it a lot easier to play around with configurations once you work out how to use them.
The other idea I have is use a piece of graph paper and do a rough sketch of a layout you like (so for example, using 4 boxes=1 foot, you can layout the table alignment easily (a 4x8 would be 16x32 box rectangle), then you can rough in the track using the known sizes of the track pieces (I did this with my layout, for curves I used a simple compass). Once you have a rough design, you can scan it and upload it here and people will give some darn good feedback on it.
A 4x6 should be big enough for a decent yard, using the kind of track you are talking about, you could also probably have some industrial spurs there outside the yard area, depending on how big you make the yard. I also think using lionchief is a great idea, it is relatively easy to wire it, a lot of lionchief engines will run on O31/O36, and your son will love using it I think.
