Use Word and Endnote. But more importantly, USE A TEMPLATE. Most universities have one for preparing doctoral dissertations. If you're a Mac user, you must download "Papers" which is the most useful program I have ever used.

Always remember that your PhD is just a stepping stone to your career goals. Considering you are going through this now i.e in your first year I would suggest tackling the situation immediately. You must tell your advisor in person, at the earliest possible time,  that either you are considering leaving or leaving for good. Advisors are understanding and this situation arises more often than you actually think. Forget about guilt. If you're unsure about your PhD plans this early in the game, the rest of the upward hike is going to be confusing, depressing and extremely frustrating for you. Good luck.