Welcome to the hobby! It sounds to me (like most of us model railroaders) that you have a very loooong list of things that you want to do...maybe too many things for the area that you have on a 4' x 8' sheet of plywood. That is not to say it can't be done, but do you really want that or should you modify your plans according to your priorities?
Do you really want to run 2-3 trains on a 4' x 8'? If you do, you may find that you will want to explore DCC. It simplifies your wiring and you won't have to buy three power packs and all the switches for block controls. etc. Yes, you will have to buy decoders for your engines and the power system will have a higher initial expense; but this will be offset by the increased flexibility and fun of running trains--not track. (I have both a DC HO layout and an DCC N-scale layout. I have hardly touched the HO layout since I started playing with my N-scale.)
Unfortunately, you have already started buying Bachmann, HO which may not be the most reliable or DCC friendly equipment. (Not my choice, but I've already been there and done that.) This is, however, a start in the hobby and you will learn a great deal from the experience you will get working with it. Everyone learns a lot building that first layout, and you won't be an exception. Many things will change (and improve) with each layout that you construct.
You have a young engineer to think about, so HO is a better choice than N at this time. That being said, you may wish to consider N scale for the future because it will allow you to do more of the things that you mentioned that you want to have--and on a 4' x 8' piece of plywood.
What should you do? Only you can decide what is best. Ask questions, read books, and try to have a plan before you get too financially committed.
What would I do? Since you have already begun, I would hold off on buying much more until you have weighed all your options. Buy only what is necessary to make a basic oval with a couple switches for industries and keep this first 4' x 8' layout VERY SIMPLE. Keep this first railroad for your little one's enjoyment. Teach respect for the equipment, but don't get upset when something gets broken...it will; and accumulate items of quality for the NEXT layout...the one that you both can enjoy. The one that you have both planned for when you outgrow the original.
Enough rambling. I have tried not to appear to be too opinionated--even though I am.

Hope this has helped. I'm sure others here will also want to bestow on you their "pearls of wisdom."
Have fun,