When I've filled dampers that were removed from the forks and springs.
I've only ever filled the original "sealed" dampers, not FAC dampers. With those, after I've drilled and drained them, I just use a tiny funnel (cap from a gear oil bottle) to refill it. I push the damper rod the whole way in and then pull it out slowly as I fill it, keeping the "funnel" filled the whole time, drawing the oil in. Once it's filled I cover the fill hole with my thumb and push the damper rod back in. If I've filled it with too much, the excess will be pushed out.
FACs will likely require a different procedure.