All,
Having spent more than my fair share of time in college working retail and fitting people into hiking boots I recommend the following:
When measuring your foot size in the store and it expands a half a size or more between sitting and standing you should get some type of orthotic. It is this expansion that tires your feet out and can rub and give you blisters and other problems.

You shouldn't use orthotics to take up volume in your wading shoe if that is your only problem- the real shoe fitters carry a hard rubber insert that you would place underneath the orthotic to take up room in the boot. They commonly refer to these as "8 iron" or "9 irons". Check out any legit hiking boot store that sells Asolo or Vasque and they will have these. There is a store in Tucson called The Summit Hut that can mail these to you and they have a flat rate shipping charge. They have an internet site.

I personally prefer orthotics called Superfeet for my hiking boots and have many pairs of them. Regardless which brand you use, these are not necessarily made to be submerged so I advise that you remove them at the end of the day so that they can dry out. Some of these products are designed with material to absorb (foot) wetness so they will hold onto the water and could end up mildewing in your boots.

Also if you go with the higher end orthotics make sure you work you way into them by wearing them (in your other shoes) for an hour a day and gradually add time. If you bruise the underneath of your feet it can take weeks to heal and you could ruin a trip by doing this.

Also I wear a good quality very thick sock (by Thorlo or Smartwool) inside of my waders which takes up room in the boot and cushions your feet. I recommend adding this "cushioning" first before orthotics and see how your feet feel. If you feel you need something more then go with the orthotics.

Enjoy!
AZ