I've done this too using the factory boot, adding wires as needed for interior lights etc.
Removing the boots and any existing wiring harness from the door shell makes it infinitely easier to stuff extra wiring through the boot. Do be advised any factory-installed harnesses are somewhat secured to the boot itself, once you have one apart you'll see how this is accomplished. Good news is its easily defeated as that's somewhat necessary to run extra wiring through them.
Using a bit of silicone spray lube helps with reinstalling the boots in the door shells. After you've done one or two they actually seem easy.