Welcome to FlyerTalk. This is a great resource...you definitely came to the right place. Here are some answers to your questions:

-You can upgrade virtually any fare on American Airlines with miles/electronic upgrades. The only exception is award tickets and certain consolidator/deeply-discounted tickets.

-You can use miles to upgrade the entire itinerary, no need to use electronic upgrades.

-As long as there is inventory in the correct fare class, you can confirm the upgrade when booking.

Hope that answers your questions.