I'm trying to replace hooks on a Rapala X-Rap Shad.  I found the bait and the hooks were gone to begin with so I have nothing to compare it to.  The Rapala website says its supposed to have one size 5 and one size 6.  But which one goes where?  Is the front hook the bigger one or the back hook?

Usually bigger in the front.

K.  Thanks.  Just out of curiosity what difference would it make?  Would it change the bait's action if I did it the other way?

Usually bigger in the front.

Yep, 

I've read that a Bass likes to attack the head of its soft prey in order to stun it and in a lot cases this holds true for crankbaits and soft plastic worms. That's the reason for a size larger treble up front. I'm sure when it comes to Crawfish they probably take a different approach.