I hadn't thought about using the original box(es), but here is what I do.
I went to Office Depot or Office Max and bought 3 or 4 plastic 'crates'. A large one that holds everything, then small ones of various sizes. They all have a simple locking top (kinda loose, so don't shake too much). I have all the dragon scales in one, and we just shake it up and use the lid as the discard area.
There is one larger than that, which houses all character, alt ending, toad, etc. that size cards. I got a small plastic (somewhere around 4"" by 10 or 12") fishing tackle box. It has little plastic tabs so you can change the size of each 'compartment'. I've set it up so that it has 6 compartments to hold: all strength, craft, fate, gold, lives and dragon slumber tokens. I remove the lid (plastic snaps) when in play, but it seals good when not.
Now for all the decks, I use another, larger size tackle box (probably something like 8" by 15" ). Once again rearranging the tabs I have a very long row for all the Adventure cards - 450 whatever of them. I can create tabs to put almost all decks in their own space and I try to keep similar together, so the three Dragon decks are in the same area, spanning 3 rows. I can have a separate row for Quest cards, Rewards cards, which are next to each other, also. Dungeon cards and Highland cards are next to Adventure, but don't need a row as long. Behind the Adventure are the Spells. All alignment cards go in one small row, likewise the rest; Dungeon Rewards, Highland relics, Lycanthrope cards, Purchase, Stable, Talisman.
You only get so many tabs so I may not be able to demarcate future decks (City, Forest, etc) but there is certainly room for all that and probably any other special decks that come up. Of course the cards are all 'standing' upright.
The game does not travel, so I rarely close the lid; I'd have to take the cards and lay them down in some fashion to reattach and close the lid. This would be the one down side, minor, as you'd have to shift the cards around out of their compartments to close/store/travel.
I was using the crates mentioned above for character figures, toads, dice but got a simple metal desk 'tray' that has several big compartments and then some smaller ones. I use this to 'sort' the characters. All the evil in one, good and neutral in 2 others. It makes it a little easier to find your character. The Reaper and The Werewolf have their own small compartment and any future NPC(Toad King?) could probably fit too. The dice are in another. (and I've added one red and white dice, Werewolf, Reaper, which we use for those rolls). I think I covered it all - Dragon Lord Crown token goes in here too.
In addition, all the rules pamphlets are in one pocket file folder. I use several acrylic plastic display or card holders for the WW and Reaper cards, so they stand and don't have to be picked up from the table. All of these fit into the large crate, except the tackle box for all cards, but it lays nicely across the crate, which is never closed anyway.