If it's a room-only code, then no, you cannot apply it to a package. Typically, when a new code comes out, they'll offer a room-only discount code and a corresponding package discount code.
The package discount code will typically not offer as big a savings off the rack rate for the room -- which makes sense because the package discount code will instead offer money savings off the meals and/or tickets.
If you are planning to stay at a deluxe, the room-only discount may be the way to go. If you are big into sit-down meals and/or like to go to Disney quest, water parks, and hop parks, the package may be the way to go.