Need some help and ideas on wiring a new layout

When you have the transformers properly phased, you only need to isolate the center rail from one loop to the other, and on each of your sidings. On old tubular track, you would use a plastic pin in place of the metal pin. With Fastrack, you can get special isolating sections, but I think there are other methods you can use as well.

Think of the center rail as the "hot" rail. Wherever the hot rail gets power, the train will move.

The outer rails are your "neutrals" and they can all be connected together to make things simpler.

You can control when a section of track gets power by isolating the center rail of that track where the section begins and ends. Then you pick a transformer and run a power wire to the center rail of that section.

Each of your main tracks will be a separate section. Each siding will be a separate section. It might help to use colored tape to mark each section on your layout as you are wiring.

When I wired up my layout, I connected each main loop to its own transformer. Then I built a bank of toggle switches, and connected the center rail of each siding to its own toggle switch. I connected the bank of toggle switches to one of the transformers.

If I want to pull a train on to a siding. I turn on the toggle switch to that siding. Then I run the train on to that siding. Then I turn off the toggle switch to that siding.

If I want to pull a train out on to the main track, I turn on the toggle switch to the siding where that train is parked. Then I run the train out on to the main track. Then I turn the toggle switch to that siding off.

You can only park one conventional locomotive on each isolated siding. You need to have one parking siding for each locomotive on the tracks if you want to operate without having to manually intervene (aka "the hand of God").

If you go with common sidings (that connect to both loops) consider 3-position "Center-off " or "on-off-on" toggle switches to route power to the "hot" rail.  So with the switch in the center "off" position, the siding gets no power and you can park out-of-service engines. Flip the switch one way and the siding gets power from one loop.  Flip the switch the other way and it gets power from the other loop. 

You could even wire up some strategically placed lights near the joints to the main loops so that one bulb/LED (or color) turns on when the siding is powered from loop #1, a different bulb/LED (or color) when powered by loop #2, and both off when in the center-off position.