You're not going to like the simple answer: Search engines aren't capable of reading Flash. If your entire site is flash-based, search engines won't be able to read any of your content, and they won't include you in any search engine results (although they'll know about your site just as soon as it's linked to from anywhere on the web).
I'm starting to see this work, with some Flash menus being followed and content indexed in Google. Of course, Yahoo, MSN Live and others are not there yet, so Flash is still invisible to them and they are still a good portion of search traffic.
There are also some techniques for combining XHTML and Flash, putting text content in HTML and controlling display via Flash. Given the text content is in the HTML stream, it can be found and indexed by search engines. See http://www.mikeindustries.com/blog/sifr/
However, if you are serious about SEO, I would avoid Flash except for specific modules within a page surrounded by content that uses traditional SEO best practices. Even though Google is starting to crawl Flash, it is still very limited and does not rank nearly as well as text content. Not to mention Flash still won't work with Yahoo and MSN. Also, playing games with Flash to display hidden text content risks all sorts of penalties for spam, hidden text, etc, so I would avoid that as well.