I have a megatech merlin which has been around the house for a number of years and never flown. I now have it together with radio trimmed. I need to put the prop on. I have an extra drive shaft , prop and a total of four nuts. One side of the prop is recessed for placement of the nut. The drive shaft is mounted. In what order do I want to mount the nuts and prop. What placement should the recessed portion of the prop be. Recessed close to the plane or far away? Any other suggestions would be helpful. I have a flight simulator, I can drive boats and cars well.

Driving R/C boats and cars well is one thing, flying a plane in 3 dimensions is another. Your skills will help you but take it slowly and shoot for a lot of straight and level flying, clockwise and counter-clockwise, after you get it up a "few mistakes" high.

I can't help you specifically with the Merlin because I've never owned one but I'm sure someone knowledgable will chime in and help you out. Have you checked Megatech's website for a downloadable manual for the Merlin?

tekajo, I think what your asking is how to mount the prop on a threaded shaft, so we'll go with that, first you put 1 nut on the shaft and run it down till it bottoms out on the end of the threads then snug it, then slide the prop on, from what you described the recessed part of the prop would go to the plane so it sits over the nut you just put on, most props have the size stamped near the hub, you want that facing out, then put a small washer and the second nut on the shaft and tighten it down, there you have it, ready to fly.
aeromite is right, fly a plane is nothing like running a car or boat so go easy on your maiden flight, give it full throttle and a good strong throw straight and level and let it climb up to about 80 to 100 ft before you start turning and make your turns nice a gentle untill you get a feel for it, remember we all crash so don't let it get you down
Good luck