Usually you can add them into the aircraft.cfg file. There should be a section in there for lights... there will also be a few numbers on each line... those numbers correspond to the x y z placement of the lights. A lot of the time it is trial and error... you can eyeball where the lights are placed and tweak the file accordingly.
The beautiful part is you can keep FS open while you make adjustments to the cfg file. Be sure to SAVE the file then reload your aircraft to see the change.
It takes a little work to get them all right but keep at it.
If you post what planes are missing lights and it is something I have I may be able to copy paste the lighting section for it. I bet you may be missing the whole lighting section if you are not seeing them at all.
Hope this helps.