So spent some time looking around the internet for a nice primer on installing DCC decoders to answer the basic questions you are asking. The ones I found were not great, although someone somewhere should have written one.
Most give you the basics on find and isolate and test the power pickups.
Next do the same for the motor.
Here's where most advice kind of goes away... it's either just "hook up the lights", or change to LEDs
Other than model specific advice, here's some of the missing stuff:
1. first, before I even start the conversion process, I evaluate the lighting setup, and see what are LEDs, what are incandescents, and if there are any "special voltages" present. You can do this by putting it on rollers, run it on DC and max out the voltage and measure the voltages to the lights (forget LEDs here for now).
In your particular example, often Accucraft hides a 6 volt regulator somewhere. At this point you will also probably discover that the 3 terminal regulator has one of the connections "Grounded" the to metal chassis of the loco, a real warning sign.
So, my take is you have to develop the lighting "strategy" BEFORE you start cutting and ripping out stuff.
Once you know what you are going to do (change all to LEDs, or figure a way to support a 3 volt incandescent), then I proceed.
I disconnect the lighting, so whatever I do next won't blow it up.
At this point then I do the track pickups and motor, and then check out on programming track, and if that checks out (can program, motor "bursts" when programming), only then does it go on the mainline and get tested out.
Only when it runs perfectly do I go on to lights.
Now I normally try to go all LED, since they are low current, no issue with a decoder and all you need is a "current limiting" resistor inline with one of the leads to the decoder.
When I "keep" an existing incandescent lamp, I usually calculate the current (remember you measured voltages before) and see if I can use a big resistor (because they normally make heat, or I have to do something else to supply the voltage it wants. This is where you have to get creative but also calculate power.
Example, you have a 3 volt incandescent bulb, and it drew 200 milliamps, and you wanted to just power it from the decoder, and you have 24 volts on the rails, then your resistor needs to "use" 21 volts, you may have an issue. The resistor will draw 0.2 * 21 or 4.2 watts !!!! This means you need a 8 watt 100 ohm resistor!
So you need to find alternatives, and check things out before you just hook up lamps to a decoder. The regulator in your loco may indeed be for an incandescent lamp, or to allow the lamp to go to full brightness "sooner" on analog.
Anyway, there are solutions (in the above example, you can usually find a 5v common on the decoder and then the resistor only needs to drop 2 volts, and that only needs a 1 watt resistor since that setup only draws 0.4 watts.
So, after all that, the #1 thing you need to do is "survey" your lighting and see what kind of lighting you have and how it runs.
Greg