Good for you! You will do just fine. There are some great hints on this site, like putting the wax ring on the flange (on the floor) instead of on the toilet.
The hardest part about setting a toilet is lining up the bolts, in the flange, with the holes in the base of the toilet. Might want to practice without the wax ring a time or two - not impossible, just awkward since you are leaning over, holding a toilet, and trying to look through one of those little holes to aim it for the bolt. If you are reasonably strong you will do OK. Some people take the tank off, which makes the toilet a lot lighter, and then you will need to replace the rubber washers on the tank bolts.
RE: the smell - I would suspect that your hydrogen peroxide mist would work here, too. You should still have whatever flooring material you have going under the toilet, so if you have tile, vinyl, etc. it'll be pretty easy to clean up. If you think urine has actually made it all the way to the wood around the flange, you might want to try a diluted bleach solution. You will also want to check the wood to make sure it's not rotted- just poke a screwdriver into it a few times to make sure it's not too soft.
Good luck!