Whipped up a test module very quickly before I gave an answer. Assume all decks are set to “Reshuffle: Never” so they’ll have a fixed order to them. If you have an origin deck with 5 cards in it, arranged with the highest value card on top and lowest on the bottom (5,4,3,2,1) and apply a send to another deck command to it, the cards will be in reverse order when they land in the destination deck–lowest value card on top (1,2,3,4,5). Last in, first out method applied to the origin deck.
As noted above, GKCs are for applying to pieces, and Global Hotkeys are for applying to components (toolbar buttons, decks, other non-piece things). You can do what you intend with GKCs, but not by attempting to have them invoke deck commands–rather, the cards (i.e. pieces) in your decks would need to be configured to act upon the received GKCs with various traits–Return to Deck, Send to Location, Triggers, whatever you need to have the pieces move themselves around to the right places.