Like Chris says, normally I strip all the existing stuff from the ceiling and just stick the LED strip up there. For full some cars, I've been known to use the plastic assembly in MTH cars to hide the LED's from side view.
A few threads on LEDs in passenger cars.
LED Lighting Upgrade for MTH Full Dome Car
Passenger car LED lighting (Again)
Passenger Car Lighting Experiment
MTH Amtrak Superliner LED Upgrade in Pictures
Notice how I used the plastic bulb holder strip to hide the LED strip.
For observation cars with markers and/or tail-lights, I tap off the LED strip and use a current balancing resistor to adjust the light level of the added LEDs.
Here's one of my heavyweights lit with yellow LED strips, really looks like the real thing.
