I've been doing this for a while, and it works out pretty well for me...
1) All of my Rares and Holos are stored in separate 4-pocket binders, separated by set. Like, I have a different Rare/Holo binder for each set since (I think) Delta Species. This includes every RH, Shiny, Secret, and LvX. In each of these binders, I sort them first Rare-Holos sorted by number, then Rares sorted by number, then RH-Rares nominally sorted by number, then RH-Trainers nominally sorted by number, then RH-Uncommons nominally sorted by number, then RH-Commons nominally sorted by number, then all the Shiny, Secret, and LvXs go in the back one or two pages. You can fit something like 8 cards in each pocket. I also double-sleeve every holographic card (i.e. I sleeve them, then put them into the pocket, double protection.)
2) Long ago, I obtained a large quantity of 400-count boxes. It turns out that these are the perfect size for a single Pokemon set of Commons and Uncommons, with 8 of each U/C maximum. Believe it or not, I can fit something like 530 cards into these boxes, and the only set that I had trouble fitting everything in there was Legends Awakened. I sort these boxes by set number and label each box with a Sharpie. I keep 8 of every Modified U/C Pokemon, and 4 of every Unlimited U/C Pokemon.
3) T/S/S/EnergySp get their own set of boxes. I separate out my Trainers based on "category". (Trainer, Supporter, Stadium, TM, Tool, TGI, etc). Currently, my Modified TSS collection takes up 2 separate 400-count boxes, and my nonModified collection takes up a single box. Unless the card is particularly good (Bebe, Rosey, Candy, Cyrus), I keep 8 of each card if it's only found in one set, and no more than 4 from each set that I can find, where 1st edition cards are treated as a different set.
4) Every card that goes over that maximum gets tossed haphazardly into a 5,000-count box, which I bring to League as a "Free Trades" box. Basically, in order to take a card out of this box, you need to leave a card. I generally don't care what kind of card you put in or take out, just as long as it's card-for-card.
If there's a vendor at Nationals that's buying cards, I'll then empty the 5,000 count box of all non-Modified cards, as well as cut my non-Modified set boxes in half, and sell them. I'll use the money to do something nice for my League, such as a free tourney with good prizes, or a BBQ, or some kind of party, not sure what I'll do quite yet.