For mass production, a plated-through hole method is used. Basically, a CNC machine drill the holes in the desired location for you accurately. Then you place the substrate into a tinning tank where side walls in the hole are tinned, at this point you have connection between the top and botton layer. You can fill up the hole with solder to block them up.
Trouble is with this method you need two equipments which can be expensive.
While I sticked with threading the wire through the holes and solder the joints. I have threaded over 3000 holes and still counting!!! Buy a pair of flush cutter to keep the surface flat at the soldered joint when removing the wire.
Due to the need for a good soldered connection, the wire must be best fit through the holes. However, you might struggle to push the wire through at times, so this is what you might like to do:
1. before threading the wire through, cut the end of the wire with a cutter at an angle to give a tapered finish (or a sharp needle). You will find it go through easier.
AND IF NOT
2. Clamp the wire using the worktop jig and pull the wire slightly thinning it by stretching. And repeat step 1.
Kind regards.