Supplies go to the skyland where the trade goods are sold or the patrols are defeated. Supplies earned by Independents and Flight Schoolers go to the faction who controls that skyland. For those in other factions, 50% of their Supplies go to their own faction on that skyland and the other 50% go to the faction who owns that skyland. If it's a faction member on a skyland owned by their own faction, all the Supplies go to their own faction.
The Supplies earned by trading are based solely upon the sales price, not the buy price or the profit. The following chart shows estimated values for the number of Supplies earned per crate at each color level.
Supplies are only earned from combats when they're fought during a patrol, and only certain combats earn Supplies.