Default rule is that playing cards are provided within the box and players pick from them in the usual random way. Also when they turn the card face up, they play the the side of the letter which is up (i.e. if A letter on the card is upwards they play A)
From my personal experience and based on opinions of people I play it with - It doesn't matter if you mix A and B together. B side is intended for advanced players, A is intended for beginners (with A side Giza and Rhodos as ideal starting wonders for novices).
Sure, we may argue that B side is stronger and, in the hands of experienced player, it probably is - but the main game "magic" happens through card deal and player's actions within their chosen strategy.
Also it is a matter of personal preference - e.g. I love playing for B side of Babylon, which most of the people I play it with do not like.
As for the third question - no, not really, as it makes only minimal difference for the base game without expansions, which I believe that you refer to. What we do sometimes is that before we choose wonders to play, we randomize an order in which we sit around the table, as we believe, that particular people as your neighbors in the game can make difference.