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I dont think there is a RIGHT way as such...
If you mean in terms of accessibility there are some basic good practices to follow - see the W3C Guidelines for Accessibility.
The rules I follow in building sites is that if the flash content is a menu or holds vital information for visitors, I offer a text alternative (this will cover for those with screen readers, and or those with flash blocked)
Mostly though I use flash to enhance my sites , i.e. not for the navigation (unless there is something a client wants that can only be done using flash) and build using CSS, I find that I can get some very nice results intergrating both tools.
One recent example - I made an interactive quiz for a charity who support people suffering from genetic disorders, the quiz was built in flash, but I also made sure we had a text alternative availible with the same content..
If I have missed your point, let me know and I will try again...
Best of luck