Make sure scannermaster is selling you a Larsen or Laird NMO mount. Beware of Tram/Browning/Cheap Chinese antennas.
A good source of this stuff is the Antenna Farm:
The Antenna Farm, Your two way radio source
As for installation….
You need to have a 3/4" hole saw that is designed for drilling sheet metal. There are specific antenna hole saws which can be a good investment if you plan on doing this more than once. If not, you can use a standard hole saw or 3/4" chassis punch. Be -really- careful if you feel tempted to use the "Uni-Bit" style "Christmas Tree" bits. They can grab the sheet metal and make a quick mess of it.
If you can, remove the head liner, especially if not using the NMO specific hole saws, which have a depth limiter that -usually- will prevent it from hitting the headliner.
Not sure how your car is set up but on some you can remove the dome light (if it's near the center) and access the underside that way.
As always, measure twice (or thrice) and drill once.
Use a couple of strips of 2" wide masking tape on the roof. This gives you a place to make your mark, and protects the immediate area around where you are going to drill. Measure again just to make sure….
Drill baby, drill. Go slow, it's not a race. Pretty much light pressure, slightly more than the weight of the drill itself.
When the hole is done, carefully clean up all the metal shavings. Don't leave any of them on the roof. This prevents scratches, and if you live in a location with high humidity, fog, coastal climate, etc. the steel chips will rust quickly and leave marks that need to be buffed out.
Remove the masking tape.
Install the NMO by passing the radio end of the coaxial cable down through the roof from the outside. You'll need to fish for it if you didn't drop the headliner. A long coat hanger can be handy. When you get all the coaxial cable in and not bunched up, you put the nmo mount in by dropping it in with the cable first, then move it back and drop the other side in.
The NMO install kit should come with a small tube of silicone grease. Put that on the O ring that is on the underside of the NMO nut. Take the O ring out completely and make sure it's got a light coat on all sides. This prevents the O ring from binding as you tighten the outer nut.
Using a small pair of needle nose pliers in the two holes on the center of the mount to hold it from turning, use a large adjustable wrench to tighten the outer ring. It needs to be snug and the nut should contact the roof fully. No white knuckles, but you do want it tight.
Wipe off any excess silicone grease that escaped and clean off the roof.
On the inside, you'll need to carefully route the coaxial cable. Make sure you don't get on the wrong side of any air bags. If your car has side curtain air bags, make sure you route the cable between them and the roof. If the airbags ever deploy, you don't want the coax in the way.
Route the coax down the side pillar to the floor and under trim to where the radio is. You want to be sure the coax isn't going to rub against any sharp sheet metal edges. Ideally you want the coax away from other vehicle wiring if you can. Do not run the wire under carpet where peoples feet will be. This will eventually damage the cable.
If the coaxial cable is not pre-terminated with your connector, you'll cut the coax to length, but leave a foot or two of extra, just in case. Ideally you don't want a big wad of cable shoved up under the dash board.
Install your connector and antenna and give it a try. Make sure all the trim is put back and the cable is safe. I'll usually wash the roof afterwards just to make sure I got everything off.
There are probably some videos or photo tutorials on line, just take them with a grain of salt. There are some seriously sloppy installs online and you don't want to do that. Important part is to make sure you have the right tools and all your parts ahead of time.
Done right, it'll look good. I've always felt that a properly installed antenna looks 100 times better than a magnetic mount trunk lip mount.
The hole plug that iMonitor posted above will work if you decide to take it out. You can spray paint them a similar color as your car to help them blend in, but hopefully you won't need to do that. You'll probably like the performance of the mount.
If you want to have the ability to remove the antenna for carwashes, etc. you can purchase an "NMO Rain Cap" which will screw in place of the antenna and protect the mount.
Only other thing I'd add:
Once the job is done and your antenna is installs, do not forget to periodically remove the antenna and clean the underside. You don't want moisture to collect and cause damage.
I'll stop now.
