Am sure there are several ways to go about it, but the ones that worked best for me are below;

1) Aircraft - open up the aircraft.cfg for the appropriate plane. Look for the [Lights] section, the following is copied from the FSX A321:

[LIGHTS]       
//Types: 1=beacon, 2=strobe, 3=navigation, 4=cockpit, 5=landing
light.0 = 3, -19.10, -54.15,  5.85, fx_navredm ,
light.1 = 3, -19.10,  54.15,  5.85, fx_navgrem ,
light.2 = 3, -83.60,   0.00,  7.60, fx_navwhih ,
light.3 = 2, -18.60, -53.50,  5.75, fx_strobeh ,
light.4 = 2, -18.60,  53.50,  5.75, fx_strobeh ,
light.5 = 2,   3.70,   0.00, -2.80, fx_beaconb ,
light.6 = 1,  -3.30,   0.00, 11.50, fx_beaconh ,
light.7 = 4,  53.41,   0.00,  4.50, fx_vclighth ,

Editing the bolded values repositions the effect relative to the model's center point (with the effect's name at the end of each line). The effect itself is found in the main Effects folder in FS, and you may be able to swap it if several options are offered (I believe there are 3 types of beacon, strobe and VC lighting available). So, if the span is 40 feet across, with the wingtips 10 feet behind the model's center, then the wing nav entries would read:

light.0 = 3, -10.00, -20.00,  0.00, fx_navredm ,
light.1 = 3, -10.00,  20.00,  0.00, fx_navgrem ,

...the third entry controls the vertical position of the effect.

As for scenery, a physical light part needs to be created and added to your structure. The part's properties can be edited to create a beacon-type light, for example. Simply create a low-poly part, such as a 3-sided pyramid, assign it the properties of the required type of light, and it will display when the project is compiled. There are decent tutorials in the help section that deal with adding lights to scenery. One last item - if compiling using FSDS3, the conditional option (such as time of day) is no longer available, meaning your light parts will need to be controlled using an XML gauge (this  code being added into the MakeMDL.txt file before compiling).

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The *practical* answer is that yes, the model's center IS the 0,0,0 point of your model.  As a rule of thumb *most* modellers will leave the 0,0,0 point to be their models data reference point AND center of gravity.

You will find, however, that some models (take a look at (I believe) the default Cessna C-172) have their data reference point at other than the model's 0,0,0, so that all coordinates are from THAT point, rather than the model center.  (Which is why the Cessna points are all negative lengthwise.)

Depending on which version of FSDS you're using, parts that you tag as "reference"  (such as your gear.center, gear.right, etc) are written to a refparts.txt file in the main FSDS folder when you compile the model.  You can create small reference parts and place them in the "lights"  positions, and then use the resulting coordinates from the refparts.txt file to "fill out"  the positions in the aircraft.cfg file.

Note that the default reference parts (pilot.view, gear.left, etc) are actually written to the aircraf.cfg file when you compile from FSDS.  Basically I use the additional tags to get a listing of the "other"  parts'  positions.

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Just create a new small disc, tag it with the reference part name Part->PArt PRoperties, and choose the desired reference part name, tag as "reference part", hit enter, and then move the created part to the correct position.