So for this mechanic to work, you would have a 60 card main deck and say... a 12 card sideboard or "PC Box"? Pick 6 cards from your PC Box, shuffle them and then place them face down as your prizes. Honestly sounds like a really fun side event. And if you use the rule where you gain a prize for being KO'd, have an errata for cards that count your prizes.
Oh, and ban greedy dice.
EDIT: Actually if drawing a prize for being knocked out is followed, Teammates would also likely be banned, at least from the PC Box.
I am apparently having a very "thick" day, so please forgive me if your post wasn't in response to mine. >.>
Earlier I expressed that an actual Side Board/Deck is no good for Pokémon, at least barring a radical overhaul in card design and card pool because too many cards can be effective counters disproportionate to their cost. By revising the rules so that a player could select his or her six Prize cards from his or her deck, as opposed to just placing them blindly from the top of the deck after drawing an opening hand and resolving mulligans, one's Prize Cards could function as a Side Board. As @Chancewoot pointed out, players have the option of running up to six TecH cards and selecting them as Prize cards. I am not advocating a larger deck size or further alterations to the rules; just if you've been hankering for a Side Board, build your deck as small as you can (you were going to do that anyway XD) and put your TecH, your spare copies of certain cards, and/or cards for an alternate strategy all in your Prizes. Such things are basically what one includes in a Side Board/Deck anyway, right? Really asking; I fear I am missing something.
If I'm not missing anything, then we just keep deck size at 60 cards. After all if it was just about having more room, we could increase deck size regardless of having a Side Board/Deck. I'm not going to worry about blending it with any of the other suggestions, at least not yet.