These are complicated questions that are hard to answer in a single paragraph. Everybody on this board answers from their own perspective based on their own experience, one cruise to Alaska or several. That may not cover all the different possibilities available.
Here is my answer based on our experiences: If you can take a taxi to the port, or get somebody to drop you off, you might save a little bit by going from SFO, but since the cruise is two or three days longer it will almost certainly be more expensive. Also, the portion of the trip from San Francisco to Vancouver is probably the least scenic, and has a reputation for the roughest water. It is perfectly possible to fly to Seattle or Vancouver on the day of embarkation, and many people do, but there is a slight chance of flight delay which may mean you miss the entire cruise. Travelling to Seattle the night before and staying in a hotel, then taking the ship's transfer or alternative transportation to Vancouver, works for us. There is usually no need for a post cruise package unless you want to.
Note that all these are generalities, and there are many other options that you might want to consider, far more than we can easily discuss here. The very best advice I can give you for answers to your particular questions is find a good local Travel Agent who is a CLIA Accredited Cruise Counselor (look for the agent's diploma on the wall, not just an agency sticker). Ask your friends and co-workers for a recommendation. The service is entirely free to you. ACC's are trained to find the very best cruise for you, after learning your personal situation and preferences, and work hard to get you the very best rate.
You can check out some of the options we have used in our eight cruises to Alaska at the page in my sig below.