Well AC and 3 rail is a lot easier than DC and HO as far as track wiring goes. No polarity issues, reversing loop or switch issues to worry about. Transformer phasing with 3 rail is a very good idea though.
A SPST switch is what I used for my sidings. 10 amps should cover most anything in O gauge. On your track plan I would still consider switching all of the sidings while you are wiring things. You can always leave them powered if you want, but still have the option to turn them off if you want to park an engine sometime and keep it's clock from running.
I am not real familiar with Realtrax, but it has a metal strip under the track at each joint that connects the rails for power and common. You can bend this out of the way or put some tape or cardboard on the center between where they touch at the rail joints so they do not connect. I have not done this with Realtrax (only read about it), but others here have and maybe they will report on a better way? I don't know if the two outside rails are connected to each other with Realtrax or not, but you can easily check that with a meter.
I think you are saying you have 2 of the Z1000's? These should be used without their Z-Controllers when powering your TIU channels, just the brick only. Also the accessory output of these is only 14 volts so I would not use that to power a TIU channel. I have not tried this, but if you do have 2 of the Z1000s, I think I would use each of their main outputs for TIU channel 1 and 2 and the accessory outputs for your accessories and switches. You can probably run at least 2 trains with a single Z1000 as long as you don't have too many lighted cars. Incandescent lighting would use more power and LED would use a lot less so the quantity will vary depending on type of lighting.
If you do use 2 TIU channels I would also seriously consider powering your TIU through it's Aux power port with a Z500 or a wall wart. The DCS book describes what you need for power for the TIU Aux port, I don't recall the rating for it without looking. I have a Z500 from an MTh set that I am using for TIU power.
Adding a TVS diode to your terminal block feeds is also a good idea and will help prevent voltage spikes to your electronic engines. There are many threads here on the forum about TVS protection that explain it much better than I can. If you are interested in using them, a 1.5KE36CA is a good choice and has been recommended here by many forum members. Here is one from Digi-Key 1.5KE36CALFCT-ND. Digi-Key has very reasonable USPS shipping for small orders.