Hello, all questions are good questions.

I dont know if this will help you but, i will give advise anyway.

I have the the Pro flight yoke and throtle.And this might sounds strange, but one thing that many people told me was not to install profiles.Not even the software that cames with the Joy.

When i got mine i instal the software, and believe me i had loads of problems, from wrong keys setups to strange behavior from the axis.

What i would do is, let the windows detect the X52, and then inside the flight sim work your way to the best setup.
I know we like to instal and fly, but thats my story.And now it works fine, i know what keys to use and how to use them.
I dont know how much this can help but its my opinion.

I give you a few links so you can read and choose the best option and its good for you to see some other opinions.

But read this it might help you better

http://flyawaysimulation.com/postlite25404-.html

http://flyawaysimulation.com/postt23437.html

http://www.saitek.com/uk/supp/x52pro_support3.htm

http://www.saitek.com/uk/down/x52pro.htm

http://forum.racesimcentral.com/showthread.php?t=283076