It is easy to run control wiring with bars mounted on the bike or keep the
foam on them and there will be less chance you will scratch the finish.
On some bikes the wire loom plastic cover is very thick and loose and
will not feed through bars easy, remove plastic cover and use new
heat shrink tubing to cover wires. This is easy to do and heat
shrink can be purchased at your local electronics or hardware store.

Location of plugs are as follows:
ROADKING: Inside headlight housing.
FLHX, FLHT, FLHTC & Ultra Classic: Inside Faring
ROADGLIDE: Inside Faring
INSIDE ROAD GLIDE FARING PHOTOS
SOFTAILS: Under Gas Tank
DYNAS: Inside Frame Backbone
Sportsters: Most are inside headlight. Some are in between risers
WARNING
THE MAIN TOOL REQUIRED FOR THIS IS PATIENCE.
IF YOU GET FRUSTRATED, TAKE A BEER BREAK AND TRY AGAIN.

Feeding wires through bars here
                                                                                                               

FOLLOWING IS PLUG TYPE FOR 2007 - PRESENT MODELS.
Instructions for 1995 - 2006 models are near the bottom of this page.

 DRAW DIAGRAM BEFORE YOU DE-PIN THE PLUGS.

Harley part number bla, bla, bla (paper clip).
What works really well is a small jewelers screwdriver.
Most everyone that has a tool box has a set of these. 
Insert paper clip into small hole, you will feel a release mechanism.
Push and presto. Wire and pin pulls out back side of the plug.

Feed the wires through the bars and put plug back together in reverse.

 FOLLOWING IS PLUG TYPE FOR 1995 - 2006 models.

MAKE SURE TO FOLLOW THE SAME RULES AT THE TOP OF THIS PAGE

THESE ARE THE PLUGS LEFT AND RIGHT

SMALL FLAT SCREWDRIVER PRY UP ORANGE CAP (BEFORE)

UNDER ORANGE CAP EXPOSING PINS (AFTER) 

SMALL AMOUNT OF PRESSURE ON WIRE TO BE REMOVED

EACH PIN HAS A LOCKING TANG. MOVE AWAY FROM PIN

PRESTO, WIRE COMES OUT BACK SIDE

Feed the wires through the bars and put plug back together in reverse.

Info provided by HD Bike Parts