First step is to download and install TweetDeck or something similar (there are a couple of options, I'm sure people will rec them here but TweetDeck I think has the best array of functions) this will turn Twitter from a difficult to manage website into a sort of real-time public chat/messaging system.
1) Whether or not replies and such end up on your feed depends how you set up the feed. If you have it linked to your account through a specific widget then only your tweets should hit the feed. However, no doubt you've noticed some other options like what weblit.us has set up that pulls in tweets by hashtags. Anytime anyone tweets anything labelled as "#weblit" it shows up on their feed. This can be useful when you want to attract attention to a general topic, less useful for individual organizations/people.
2) Following a lot of people -vs- not. Before Twitter took off and a bunch of apps were written to auto-follow and spam, following a lot of people meant something. Now it means almost nothing. The key with Twitter is to build relationships, to build up your networks and access more people. For example, without twitter I never would have gotten to know Jan or am_harte or half the weblit community. Emailing a stranger is awkward and almost no one emails back, tweeting is different ... even famous people will tweet back to you. String together enough little conversations and you've built a relationship that you can leverage to promote your projects. When I tweet about a project update or (more likely) a new essay about weblit as a business, all those new relationships frequently retweet it so that all THEIR FRIENDS hear about my update to. This is extremely useful in driving quality traffic to the site
3) Lists are really new to Twitter, so it's hard to say what the impact will be just yet. Basically Twitter realizes that the number of people tweeting for business/hobbies far outweighs the number of people tweeting for in-real-life personal things. So if I'm interested in weblit ... I want to follow as many weblit people as possible. Lists allow me to do that more easily because all I have to do is find a weblit person, then follow their "list" of other weblit people. From my understanding-- although I haven't really played with it much-- it's like following (potentially) hundreds of people in one click. Useful for building a collection of people you want to network with.
I have to reenforce what Dary said, just remember that Twitter is completely public. There are lots of functions and options to screen out public noise and make Twitter seem like an private area but it's not.