When you change hooks on a squarebill for instance to a larger size and a better hook do you replace both hooks? What if the size you want won't work very good if you change them both, so you just change one.  Do you put the bigger, better hook on the front or the back ?

Yes.

You can go to a larger hook or just a larger one usually on the belly hook. I replace both hooks with a size larger short shank hook if I can get away with it. If I can only do one it will always be the belly hook though and a smaller better quality back hook. I like VMC short shanks and I'm a big fan of red trebles. They might not make a difference in strikes but they make a difference in my confidence and that makes a difference in how you fish the bait.   

Bigger hook on the front.