many people these days make flash websites in a few simple steps.
1. making the navigation very flashy with rollovers and rolloffs.
2. using the blur in flash 8 or cs3 to make objects motion tween in and out.
3. and using slide fade in motion tweens to make text appear and dissapear. For the most part you just have to play with the program until you get good at it. However, flash us not good software for designing things. Since this is the case, many people design the sites in photoshop, slice the images, and then make them come to life in flash.