Replacing thru-hulls is one of those projects that seems simple, but is often fraught with complications.  My experience has been that they will spin in the hull if you do not hold the center fitting.  Even when holding the fitting, I seem to always have old gate valves which are completely frozen on to the stem and have to be cut off.  I also find that the ring nut which holds the actual fitting in place will be completely frozen as well.  There are ears inside of the thru-hulls that are for holding them from spinning.  Special tools are made for this purpose. I've had good luck with very large cold chisels and even the handle of a large pipe wrench for grabbing these ears.  Then hold chisels etc. with another wrench.  I have found that what invariably happens is that you either wrestle with the ring nut and it ultimately disintegrates after much effort, or you can just drill it in two opposing spots and remove it in a few seconds.  Always use a cutting fluid when drilling metals.  It makes quite a difference in speed and bit life. 

Invariably, the wood pads which are used to reinforce the area of the thru-hull fitting are soft and should be replaced also.  Cut new pads from either marine ply or exterior ply and then use hole saws to cut a ring to make a new pad.  After all cuts are made, epoxy coat the new pads to protect against water.   Two coats should be applied, as the first will be absorbed somewhat.

Thru-hull fittings should be bonded to the hull with a high quality adhesive-sealant.  I have had good luck with the 3M products.  The only plastic fittings I have below the water line are in the form of transducers e.g. knotmeter.  All plumbing fixtures are bronze. 

The first few pictures are general.  The  remainder follows repairing a beveled recessed seat for a flush sitting thru-hull fitting.  When I removed this particular fitting, it had obviously been removed before, and it looked like someone had used a chisel and had  really torn up the seat.  The fiberglass was ripped open, the gel coat finish destroyed, and a poor attempt had been made to repair it with some form of putty.  I decided this was a job for epoxy and Cab-O-Sil. I dug out the old putty and cleaned up the seat.  Unfortuneatly, I can't find my photos of the before.   I decided I needed a form, and an old fitting just made sense.  I used some heavy plastic to keep the fitting from becoming bonded to the epoxy and Cab-O-Sil mixture.  So, I mixed the ingredients to a peanut butter consistency, placed the old fitting with the plastic film on it covered with the mix into the hull and held it firmly in place through the curing process with a 2x4 braced against the ground below.  Once cured, I removed the form and then did a second application of epoxy Cab-O-Sil mix. After the second application I used a dremel to do the final evening and fine shaping.