It gets difficult when you have specific gifts for specific staterooms. We learned this one the hard way. We packaged everything up to get onboard, and then once onboard we separated it all into shopping bags by deck.
This year we're trying something a bit different -- there will be a few distinct groupings (adults, teen boys, girls 7-12, boys 7-12, and girls 6 and under, and boys 6 and under). That will give us five shopping bags.
Between DD and I, we will follow our deck plan (with staterooms highlighted) and just dip into the requisite bags as we stealthily make our way around the ship. That way, at least, we're not digging around to find the right labelled gifts in each bag.