Much as I would love to, I don’t claim to have invented the method. It’s pretty much the standard I saw when I tried Codex out at the Fantasy Strike Expo in 2015. 
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I love that you do the same thing as me, which is also sub-sort spells, tech 1 and tech 2 by cost! I pretty much follow that as well, except for those colours that have, say, 1 building in each spec, in which case I put them to one side.
Such organization
Much everything in its place
Wow
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Those FSX boys sure know what they’re doing then. 
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To be fair, the organization of the middle pages is taken straight from the rulebook.
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I own just the Core and the Starter.
(I didn’t want to fork over all the money for Deluxe since I didn’t know yet whether I’d love the game. I love everything about Puzzle Strike on paper, but when I played it I just found it stressful in a way that never made me want to play a 2nd game in one sitting, whereas I can play five games of Dominion in a row. Turns out I do like Codex at least as much as Magic, which I don’t buy, so eventually I’ll have to get the other factions.)
I use the right side of the first page for three mono-color heroes (Mid, Cal, Arg, in a vertical column). Then pages 2, 3, 4, 5 match the layout described int he core Rulebook (spells for the spec, tech 1, tech 2, tech 3, moving right in the rows that match each character). This leaves some extra space in the front, and a full page in the back.
The extra space in the front is dedicated to a Neutral character (say River) and all their spells. The extra page in the back is dedicated to all the tech units of that neutral character. This way, I can hand over binders for new players and say, “Ignore all the green cards, just use the grey from the front and back pages.” For a more experienced player, I can say, “Ignore the grey, just use the green.”
I rubber-band a small pile of starter deck, worker card, matching spec cards, and add-ons together, and that sits in one of the card-pile areas of the core box. That way I can just hand players all the set-up cards that go with their color.
I know that the hero cards are set-up cards, so they could go in this set-up pile, but I prefer having them in the binder to begin with so that it’s obvious which heroes come with which magic and tech cards.
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Welp, Sirlin better start selling binder’s in the play store as I have found nothing that compares to them quality wise.
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I’ve got the deluxe set. Here’s how I organized it:
In each binder, the first page and the last page is empty. The middle pages are organized the way the rulebook suggests. Except: In the green binder, on the first page, I put Bashing’s spells and Tech I cards, and on the last page I put Bashing’s Tech II and III cards. I did the same thing for Finesse in the red binder, except that I also put the dancers in the first page.
I left out all of the tokens, starting decks, and heroes and I put them in the box using the colored dividers. I might switch to using a card box later.
I recently sleeved up my print and play of White and Purple and i find “Ultra.Pro” Pro-Binders to be quite good.
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I own the Deluxe Box. I use the front half-page of the binder for the 3 heroes, their Spec mini card above each hero, and the worker card below. The middle full pages i use as suggested in the rulebook. I keep the Starter decks in the box using the dividers, along with the colors associated tokens.
I have the Deluxe set and use the same method as Juicer.
What I want to know is - what do you do with all your binders? They are too fat to fit back in the large box.
I’d like to keep the binders all together - guess I’m going to go with a bag or tote or something.
A GoodLife fitness gym bag has worked well for me. lol
I assume Sotek is probably back from vacation by now, but if you get another extended opportunity for trolling, might I suggest:
- remove one copy of each card from each binder
- shuffle your pile of cards
- deal one card into each pocket, placing it behind the existing card.
It’s probably funniest if you do this with a subset of the cards, maybe just 3 or 4 per binder.
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This is not a prank. This is an extremely cruel form of terrorism. 
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You’re a monster. And I actually like Sotek.
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Another vote for the same style as Juicer! Didn’t look carefully but it looks like he too has his binders organized from low to high price, then alphabetized within the same price.
Unsure if anyone else does this, but I had some extra hard sleeves left over, so I put the spec minicards into one of those for each color and slide it in behind the worker card for each color : o
Not quite. I organize it by cost exclusively, except for Tech II. Since Tech II is split across two pages, in a group of three cards, and a then a pair, I tend to put upgrades and buildings on the two card side.
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I organize my binders like the rulebook suggests. It would be nice to have all faction-related cards inside the binders, but green and black just have too many tokens. Instead I made a pile of hero cards, starter cards, worker cards and tokens (in this order) for each faction and put it separately into the box. This may consume more space when travelling with something other than the deluxe box, but it reduces startup time of the games as there is no need to fiddle the starting deck out of the binder.
For the neutral factions I built my own Finesse and Bashing binders. They have less cards so everything fits on one double page. Left: Spells and Tech I, Right: Tech II and Tech III
I am using the method of TheJTrain: If you remove the inlay all components fit nicely, even two or three additional playmats.
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I’ve found that the last page of the binder makes a good place to keep tokens. Green has an abnormally large number, admittedly (Protip: if a given type of token is summoned in sets of more than one, you can put more than one of a given token into the same pocket)
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I have the first page of the binder with each of the starter cards, then on the next page I have the 1 starter that didn’t fit in the top left corner, and the worker in the lower left corner.
On the same page, I have my heroes all to the right on the page.
Corresponding spells are then on the page to the right of them, until the ultimate spell, which is on the next page. After that we have tech ones, twos and threes like the rulebook suggests ^^
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So, I have a 4 pocket/page binder, with the card openings facing the “center” and only on one side of each page.
What I’ve done is put the 8 (single) cards I almost always tech in the middle pages, so they are all visible. Then going to the right I have each Hero’s spells (one page per, stakced 2 per slot), followed by the Tech 3, the Tech 2 cards I expect to never bring in, and the starter deck cards. To the left I have 1 page with the rest of the Tech 1 cards, then one page per spec for Tech 2 cards, and the Heroes on the very leftmost page so they are visible from the front when I open the binder.
The 2x2 size fits better at the table than the larger version (plus it’s what I had)