I do that by printing "white" on clear decal sheet, painting white on the train and putting the decal over it. The black, however isn't very opaque, so you have to disguise it a bit. I used a little weathering on a caboose. Since I wanted a painted out, sloppy look, it didn't turn out too bad, though I think I should take this "prr truscan" paint and do the rest of the caboose.
My gold "Asylum Valley" lettering is the same. Since it's isolated from the rest of the car, it looks pretty good.
Otherwise, contact Stan Cedarleaf or Del Taparro right here on MLS. They'll likely chime in here shortly.