Before dunking a PCB into the copper plating solution - through-hole walls need to be "activated". This is a fairly simple process that we'll detail below.
The first step is to drill all of the through holes (TH) into the FR4. There are a couple of .125" registration holes on the bottom of our small test PCB, along with a grid of 40 mil diameter holes (IC's), 23"ish" mils for plated through hole components (PTH) - resistors and caps, and 16 mil holes for vias.
Next, break out the conductive ink, mix it up very well and coat all the holes on the primary side with it. Using a shop vac, suck it out from the secondary side - the goal here is to suck ink through the hole to evenly coat the side wall. You can repeat the process from the secondary side for good measure if desired. Note that none of the through holes should be clogged after vacuuming out the ink/graphite - if they are, they won't plate correctly.
Cure the ink by putting it in the oven at around 90 degC (~200 degF). After curing, the ink will no longer be shiny and the graphite should stay in place fairly well.
Now scrub both sides with a scotch brite pad - it's important to not disrupt the continuity between the TH walls and surface of the copper (so don't push down too hard). If there is a break here, then the walls won't plate properly. If your target is mechanical milling - the worst that any residual ink will do is contaminate the plating solution. If you plan on etching the board, then you'll want to take off all of the ink - since it will most likely act as an etch resist.
When the PCB is cured and cleaned, the graphite should be visible on the through hole walls and there should be no residue on the surface of the board (there are most likely going to be some stains from the ink). The corner of our test PCB could have used a bit more cleaning - but since we'll be milling it later on, the extra ink shouldn't hurt anything.
Finally, here's the complete gallery for your perusal: