The replacement motor/drivelines/wiring you got came from the basic rtr units, if you follow my suggestions, I'll walk you thru this. I bought about 5 sets of these off ebay myself.:
Since this is on a basic rtr unit, and not the better units, They used a shortcut here and didnt run the wires straight from the truck sideframes. Instead they used the old trucks and a lil creativity. The right side of the truck power is transferred via a clip to the top of the truck, and the left side of the rail is thru the frame via a small tab-like square with a screw in it.
I know what wire your talking about, it's a single wire with a metal tab on it with a hole/screw thru it, correct? if so, it does go to the frame. That is the one single element that hasn't changed with athearn motors and dcc boards. The left side of the rail still connects to the frame via the flat surface on the truck that the frame rides on. And by doing so it "grounds" the frame, ( ground being a dc-only term here). The dcc ready board that sits on top of the motor picks up the "ground" from the frame via the wire with the metal tab. Now this is only in reference to the early dcc-ready loco's that athearn put out. As for the board, it should have 4 sets of pinouts on each end. The pin-out is as follows, with the unit facing away from you:
far left, left side of rail or the frame
middle 2, for the forward light(s)
far right, right side of rail or top of the truck clip
and the bottom of the board is the same, jsut reverse order, but maybe missing the wire going to the left side of the truck.
I saw this in a ACL GP40 I picked up a while back, and even though it wasn't a "RTR" unit, it still had the hex driveline system in it, but with no dcc-ready type board. These units, to make dcc, you have to replace the light boards in.
I hope this helped you.