Bottom logos are laminated directly to the foam. Spread some resin on the foam, place the logo, then apply more resin on top of the ricepaper and squeegee out any air bubbles. Then the fiberglass is rolled out over it and laminated.
Deck logos go in between the first and second layer of fiberglass. Same method of applying the logo as the bottom with extra resin and squeegeeing out any air bubbles, then roll the top later of fiberglass over and laminate.
When doing a pigmented lamination you will have to apply the logo after you lam the board then lam a small patch of glass 1.5 oz fiberglass cloth over it. Once that cures you can blend the edges of the lam patch and hot coat the entire board.