If you use 100%, your flash will scale to fit the user's browser. This can cause a problem with bitmap images and text.
Don't forget that even if a user's screen is 1024x768, they do not have that much space available for viewing, as space is taken up by the browser toolbars, scrollbar, status bar etc.
Also bear in mind that lots of people still use 800x600
If you want your site to be visible to the largest possible audience without scrolling, you should set the maximum size of your flash to approx 740x480