i like having my shop on etsy, there are other handmade sites but they are not so well known outside the artsy community. The best advise I have is take great pictures. Build a small light box and make sure the pictures are always in focus. Also don't rely on etsy to advertise for you because they don't. try to list something (or re-list something) everyday, promote yourself off site in a blog or twitter for example. I have a blog, twitter, and i post ads on craigslist for time to time. also some people say flickr helps direct sales too, but it hasn't for me. Make business cards and pass them out to anyone who expresses interest. good luck
flat rate boxes you can stuff as much as you want and you don't have to worry about weight. i use regular priority boxes because plushies tend to be very light weight and it's not worth paying the flat rate fee.
i usually ship United States Postal Service Priority Shipping with Confirmation number. It is usually $5 and change so i charge $6 for shipping and handling fees. It's a little high price for some people- but I know it's the best way to ship something, and being able to give them a confirmation number so they can track their package is great. I've only ever had 1 package not reach it's destination within the 2-3 days and that was at chirstmas time. now if you are shipping stuff that is small enough for first class, i would recommend that because it costs less and takes just about the same time. you can even order FREE priority boxes and envelopes online! good luck with your shop!