First, you better put your flash files inside regular HTML files. You sure want to include some Meta information in your site for it is a really good spider food. To make it even better, also put some HTML above or below the flash element.
Spider crawl on text so put a lot of it in your flash. Don’t forget about the choice of relevant keyword. Enrich the text with those keywords. And also use keywords on the links. Spiders follow links in Flash files.
Some more practical way, create two versions of the site. The first one is the flash version you like, and the second one is just html version. Beside providing good food for spider, this version also help those with no flash player plugin of for slow connection.