Filling old motor mount holes in transom

I'm plannning to replace the old horseshoe style motor mount on my Scot with the new style of mount, and will need to fill the old holes left in the transom. Can someone point me to a good reference for performing the repair myself? I'm not sure what's involved but ready to learn. ~Nick

It's easy if you do not want to worry about cosmetics.  So, let's assume that's what you want unless you state differently.
Clean the area directly inside the hull where each hole is with acetone before you sand. Get some acetone in the holes too.  Let it dry out for a few minutes.  
Roll sandpaper into shape of a cigarette ( so you can sand in the holes - sand each hole just to give it a fresh edge ( use 80 grit ).  Blow out with compressed air or your lungs.  Clean again with acetone.  Let air dry a few minutes.
Tape the holes on the outside with good painters tape so no resin can leak out.  Tape around the holes on the inside so when you inject the resin in, it will only get on this removable tape and not on the hull.
Go buy resin ( with parafin ) called finishing resin and catalyst.  Buy cabosil ( you don't need much ) - this is a thickening agent.  Having a syringe really makes it easy ( I clean these with acetone and use them for several jobs )
Mix up the resin as described on can ( a take out chinese soup container works well ) - enough to fill the holes and then some ( do more than you need ) try not to do this on a scorching day and not in direct sunlight as heat/ temperature affects cure time.  Once mixed properly, and working quickly ( not racing ! ) I would take a Q tip or a small flux brush from Harbor Freight - dip in the mixed resin and 'paint' each hole with some resin.  
Then, add the cabosil into the remaining resin mix - add slowly, mixing, until you get the consistency of mayonnaise.
Personally, I would carefully fill a syringe with this thickened mixture and insert the syringe deep into each hole, squeezing out the mixture and slowly pulling the syringe out to assure that you completely fill the hole and leave no voids.  When you get to the end of a hole, clean the hole area of any resin, have a pc of tape ready - put tape on the bottom portion of the hole - squeeze the mixture in as it fills the very end - then push the tape closed - closing the completely filled hole.
Repeat on each hole.
Clean up any mess or drips with acetone ( use papertowles or box o rags. 
Let cure over night.  Pull tape and you'll be done.
Doing the above to match cosmetcially is more challenging as it involves gelcoat and color matching.
There are other ways, i.e. pre-thickened glaze i.e. DuraGlass, but getting used to using resin will help you down the road for many repairs.  For me, it started with fixing my surfboards - but from there I have done a lot of work - enough to save me a lot of $ in repairs.

All I did was take off the motor mount bracket, clean up the gelcoat and put in some stainless carriage bolts along with a little 5200 for good measure. Looks nice and clean and saves a lot of hassle with resin and stuff. 

West System 6-10 thickened epoxy will make this very easy.  It is thick enough to stay in the holes without the tape and cures quickly.  I would still tape on the outside to avoid a mess.  Gelcoat repair is also easy, especially with a white hull.

Thank you for all of the detailed advice for repairing the holes left by the old motor mount. It's great to have a communitity so willing to share their knowledge and experience.