There are many shops, and nearly all of them will do transfers free of charge if staying in the Patong-Kata-Karon area.

The main choice will be a 4 days course or 3 days course. The 4 day course offers the highest quality and is more relaxing, but will also cost a bit more and take more of your vacation time.

More information here.

Agree with mark, some of the instructors are here just for the experience and don't care too much about the quality of their courses, while others do care, and will make sure you learn how to dive properly.