This guide is not comedic, it's strictly for information sharing so please comment or contact me if there is anything I should add or change.

Sometimes you hear footsteps outside, that's a sign he's there and you need to flash him. However, I don't always hear the audio cue. Whether it's because of me simply not hearing it or the game not registering it I do not know.

The doctor will appear on your cameras from time to time and you need to flash the camera light on him by pressing (Space) to make him leave. If you don't, he will eventually move out of sight of the camera, and if you are still watching the camera-feed by then you will die the next time you leave your computer.

If you aren't by your computer when he enters the house he will wait in one of 3 closets in the house.
If you:
A. Use your computer.
B. Open the door to the closet he is in.
You will die.
The only way to avoid dying at this point is to hide in one of the other 2 closets.
Open the door to an empty closet, enter, and close the door behind you. Wait a while, and he will eventually leave, and then it is again safe to use your computer.

BE EXTREMELY CAREFUL with the flashlight usage on the security-cameras, as the power easily goes out from using it too long. Only hold the light if you see him, otherwise just tap it to gain visibility. If The doctor is there, you will see him moving.

The kidnapper will enter rooms where the light is off.
According to lore, the lights turn off due to "electrical malfunctions", and flicking them on and off a few times will fix the problem.

Due to this, lights will turn off in rooms at various times, indicated by a sound que of a fuse being blown. However, if the light goes in one of the back rooms there is a chance you won't hear it, so make it a habit to take a walk around the house checking lights.

If you don't take a stroll and go turn the lights on, the kidnapper will eventually start picking the locks to the windows, break in, and you've lost.

Always, ALWAYS lock the windows by right-clicking them when they're closed.
Due to "faulty mechanics", always try to open the window after locking them to make sure they are locked.

Unconfirmed
I got killed after completing a shift, got kidnapped while "lying in bed". So, I think the kidnapper will kill you if any windows aren't locked when you go to sleep, so I suspect he might unlock windows but not climb inside. So whenever you turn on lights, I recommend you check the windows in that room to make sure they're locked

When waking up

Whenever you wake up after a night, lock all windows, make sure they are locked by trying to open them, if they are properly locked you will hear a sound but the window won't open.

While checking all windows you will enter each room, so make sure the lights are on at the same time.

Mid-game

Take a walk around the house every once in a while checking all the lights, as the audio cues of the master bedroom and the guest bedroom won't always be heard when using the computer.
I recommend you check the security cameras for The doctor before and after you take a walk checking lights, as this will take a while.

Do not do this between reports as it will take too long to complete a single report, and you will most likely die by the time you're finished.

Once you have completed the report quota you will automatically go to sleep.
Once you've slept you'll wake up and do this whole thing again, beginning another night.

This guy made a really good video about it, so give it a look as he explains the basics very well.

1) default key bind is F to use your flashlight
2) close the report using the little cross like button at the top right corner. Closing it will put it back to the report desk window