I am a little perplexed as to whether or not I am landing correctly. I have read both the manual and the link presented in the FAQ section--which is very, very helpful by the way.

When I am landing, I bring my AOA from 11 degrees to the optimal 13 degrees when I flare. I land on the freeway just fine and then aerobrake--is there more to braking? The manual says to aerobrake the aircraft and then it pretty much ends in its explanation.
Here are the questions:
1) Isn't it advisable to use the wheel brakes as well? Again, the manual doesn't touch on that--I don't think so anyway.

2)When I touch my wheels to the ground, it looks like the tail of the f-16 is super close to scraping the runway; I am using 13 degrees AOA btw... Am I landing horribly, or is this to be expected? It doesn't look very pretty when my tail is millimeters away from touching the ground...

1. Why not? So far as aircraft comes down to below V1 (theoretically speaking). However, you wouldn't want to keep applying the wheel brake more than a second at a time while aircraft is still well above taxiing speed.

2. Do you bounce often after touch down? Unless you actually experience frequent tail strikes or bounces after touch down, I guess it should be OK. Definition of flare in my vocabulary is a maneuver pointing my FPM to the end of the RW just before TD to make the impact angle of TD more shallow. As a matter of fact, I hardly give a glance to my AoA when I touch down. (That is of course so far as I haven't made any drastic last minute maneuver during the final phase of approach)

There are so many different methods people use to land in this game, which I have come to find out... I, personally, prefer using the AoA Method--which is a methodical approach to landing, written by Paul Wilson--because the author says that this system is similar to the approach used by real f-16 pilots, he writes, "The system I refer to is based on the approach that real F-16 pilots use to land the real aircraft. Some of you may find that this approach is much different from the one you have used in the past. If you are interested in landing properly like a real F-16 pilot or if you are simply interested in seeing how it is done, read on!".

Paul Wilson tutorial has been there as landing 101.
I perfected MY landing starting with his tutorial in the beginning as well.

You asked, I gave my thoughts. I didn't imply you are doing it all wrong, did I?

No, I didn't even think I gave the indication that you implied anything of the sort; I was just saying that Paul Wilson's method is my current method in order to further help you all in answering my question.