Good question
1. When you sync the dual sync (Put the engine at 50 BTDC and turn the distributor until both lights turn on and one barely shuts off) you are giving it a reference point to control timing from. If it's right, it's right, but personally I would go back and make sure given what you are seeing. There are two components of checking it....setting the distributor per the instructions and second is making sure the reference angle in the program matches the instructions. For example if 50 degrees is the reference angle, you set up the distributor, and then when you power up the program you make sure the same value, 50, is in the reference angle field.
2. You should never turn, or need to turn, the distributor after that, but you may need to adjust inside the program to make timing perfect. Let's say your initial is set at 18 in the handheld, but you see 15 in the balancer with a timing light, the Inductive delay is like a thermostat that will correct it, it changes the delay in the computer to make the commanded timing match the actual timing, you don't turn the distributor. I am not sure if the handheld will let you adjust inductive delay, but it is easily done on a laptop. Also, you may not even need to do it, but it is worth checking with a light. I did not need to do it on mine or the last one on the dyno, but since you are fighting potential timing issues it's a great idea to check it
After that, you are done forever with basic setup, you will just change timing values in the computer... initial, cruise and WOT. I think it is FAR better to do timing changes on a laptop, but it takes a couple steps after you program the ECM to save to the SD card. Easy after you do it once or twice.
Do you have the program on a laptop or doing it all by handheld? The reason I ask is the Wizard is not as good as the free Sniper program. However, if you have the ability to pull your global file off your SD card, I could manipulate it for you too and email it back