Facebook's documentation process is very poor, so don't feel bad about having a hard time getting started. Their wiki-style approach to documentation without any real official documents tends to leave the "process flow" tough to grasp, and requires piecing together parts of a bunch of randomly scattered docs.
Facebook has an obligation to protect privacy, so they never make a user's actual email address available to application developers, through Connect or normal applications. They do have a proxied email system in place that you can use, however, you must get explicit permission from a user in order to email them. There's a decent document on proxied email here. You can get permission by prompting for it; there's several methods for doing so linked in that document.
In regards to linking Facebook and local accounts, this would definitely be the way to go. Once a Connect user logs in, you want to store that fact for that user so you can provide the Facebook-specific functionality. I would simply create a normal user account in the database for every new Connect user that came by, with it's own local id, so that you don't have to do special handling of two different types of user accounts all over the site. That being said, the account would obviously have to be marked as a Facebook user's account (I use an externalId column in my users table), and any part of the site that relied on information you might otherwise have locally would have to handle the Facebook aspect properly (such as using proxied email instead of normal email).
For existing users, you could arrange an "account link" by having a process whereby they log into FB Connect after they've logged into the site already, and you could detect that and simply add their FB id to your users table. After that, they could log in through Connect in the future, or through your normal process. I've never done this, but it should be possible.
If you write the account handling code generically enough, your site will be able to function well no matter what kind of user you throw at it.