In my current Conan campaign, we are using the Paizo critical hit and fumble decks and having great fun with them.
I use an account-type system to keep track:
PC draws a card after scoring a critical hit: 1 in PC's favour
PC voluntarily accepts a critical fumble card when they have a confirmed fumble roll (see below): 1 against PC
GM draws a card after scoring a critical hit on PC: 1 against PC
GM takes a critical fumble card when NPC has a confirmed fumble roll (see below) against PC: 1 in PC's favour
The GM automatically uses a critical hit card against a PC if they have a least one card total in their favour. The PC can always voluntarily accept a critical card against themself if they want to build up credit. If no critical hit card is involved, the btb critical damage multiplier still applies.
Example:
Asrod scores a critical on two occasions in tonight session, and both times he opts to use a critical hit card.
In the same session, Shrit Andaka makes a critical fumble. He has never used a Paizo card to benefit himself before, so the GM cannot demand that a critical fumble card be used against Shrit. However, Shrit's player decides to accept the card voluntarily.
Also in this session, an NPC scores a critical against Zingelito. Zingelito has never taken a Paizo card, but he wants to build credit, so he allows the GM to use a critical hit card against him.
At the end of the session, Asrod has 2 cards in his favour, and both Shrit and Zingelito have one card against them.
In the next session, an NPC scores a critical hit against Asrod. Since Asrod has 2 cards in his favour, he cannot avoid a Paizo card, so the GM draws one. Now Asrod (if he survived) only has one card in his favour.
Another NPC scores a critical hit against Shrit. Shrit has a credit of one card used against himself, so he can prevent the GM from using a card. This will bring Shrit's 'balance' back to zero.
Meanwhile, Zingelito makes a critical fumble. He can prevent the GM from using a card (bringing his 'balance' to zero), or he can tell the GM to go for it, knowing that it will be nice to have 2 cards against himself in credit.
I've made this sound more complicated than it is. I just have a piece of paper with two columns and each character's name. Whenever a card is used against a PC, I put a tick in the 'Used Against' column. Whenever a PC uses a card for their own benefit, I put a tick in the 'Cards Taken' column. If a PC has more ticks in 'Used Against,' they can protect themselves from fumble and critical cards. In practise, some PCs are very daring and gladly volunteer to suffer the consequences of the cards, knowing they will get to use them for their own benefit as a result. Other players are more conservative and almost never use cards for themselves because they fear having cards used against them.
As for critical fumbles, we use a confirmation system. If a PC rolls a one, he or she then rolls to hit again (same attack bonus, etc.). If they miss, it's a critical fumble. However, if no critical fumble card is used against them, the PC suffers no ill-effect from the fumble (asside from an embarassing description of their failure by the GM).