The classic autolyse process as conceived by Professor Raymond Calvel called for combining only the flour and water and adding the yeast (and salt) later. The reason the yeast was left out of the initial mix was because it was believed that the activation of the yeast would acidify the dough. The present thinking on this subject seems to be that if the yeast is unlikely to be activated during the autolyse rest period, it is perhaps safe to add the yeast to the flour and water. It is also believed to be acceptable to add a natural starter to the flour and water, for the same reason.
The question of the duration of the autolyse rest period is a tougher question to answer. One of our members, artigiano, recently raised essentially the same question at http://www.pizzamaking.com/forum/index.php/topic,4071.msg34114.html#msg34114
. As you will see from my reply to that post, the autolyse rest period can vary from as little as 5 minutes (the duration recommended by Evelyne Slomon for a small dough batch in a home setting) and as long as 45 minutes, although the most commonly cited rest periods are usually less than 45 minutes. My advice is if you plan to use a long autolyse rest period then it might be best to leave the yeast out of the flour/water mix. However, I might add that is not the approach that many of our members, and many professional bakers as well, follow. Many combine ingredients without regard to the classic autolyse method and some even use multiple rest periods. So, you may want to do your own experimentation to find what works best for you.