The way I'm understanding it, we are talking the difference between this: http://www.a1leasing.com/uimages/vehicle_images/5_X_8_Trailer_Image_2.jpg which is a turn signal / brake light combined style and this: http://www.xlspecializedtrailer.com/webres/Image/options/aluminum-taillight-trailer-lrg.jpg in which the turn signal and brake light are separate. In this instance, the outer lights are brake lights only while the inners are turnsignal only, regardless of running light.

With the first style, everything is run through the turn signal switch. With the second style, the inners are run the the turn signal switch while the outers are only run through the brake switch.

So the set up does matter. When he says "I put turn signals on '50 1/2 ton, and everything works perfectly; but now it's time to hook up the brake lights (by the way, have lights on both sides in rear)." to me says he added separate turn signal lights and still has to hook up the separate brake lights. The running lights aren't an issue.