Lisa
You really don't want two isolated sections. The primary reason is that transitioning a train from one section to the other is very difficult because it's impossible to match speeds and voltages between the 2 power packs. The train will jerk when it intermittently spans the gap between the 2 sections and momentarily gets power from both power packs. This is also hard on the power packs because there is a temporary uncontrolled current through the train wheels between the 2 power packs.
The better and traditional way is called "cab control" wiring. You isolate the track into a series of blocks, generally about a train length long, but at least 4 blocks per loop. The isolation is done by using insulated (plastic) rail joiners or no rail joiner or physically cutting a gap in the rail with a Dremel tool or track saw. If you use physical gaps (no rail joiner or cut the rail), most (and I) recommend gluing a small piece of thin plastic in the gap to make sure the gap doesn't close later. When the glue is dry, file the plastic so it is smooth and flush with the rail. If you are using traditional DC power packs, and have no reversing loops, only one rail needs to be gapped at each block junction (but same rail in every case!).
You then use either Atlas Selector switches or SPDT (center off) toggle switches to control power to each track block. If using toggle switches, the center terminal goes to the track block, and the outside terminals to your 2 power packs. The rail that was not gapped is fed directly from both power packs. The Atlas Selector comes with wiring instructions.
In use, you use the Selector or the toggle switch to control which power pack supplies power to a given block. You use the same power pack to control the train where ever it goes on the layout by giving that power pack control of each block as the train moves into it. The center position turns the block off - good for having an engine on the track and not powered, or for trouble-shooting and isolating any electrical problems.
The alternative to the cab control wiring scheme is what is called DCC. A decoder is installed in each locomotive and set up with a specific address. The DCC throttle selects which locomotive it is talking to, and controls it. DCC eliminates the need for blocks, since each locomotive is addressed separately. The drawback to DCC is upfront cost - the throttle(s) and installing a decoder in every locomotive.
If you decide to put the reversing loop back in the layout, please post again, and I will try to explain how to wire it.
Hope this helps, and that you had a Merry Christmas.
yours in wiring