Bots are scripts that do things on the internet (online robots). Search spiders are a type of bot, and they're how search engines find stuff to index, so people can search for it. They can read things in your html that don't show up to a person looking at the website, but they can't read flash. It's possible to add a bunch of html to make a flash site search-engine friendly, but without that the bots won't have any idea what you're about. I don't know what options moonfruit gives you to deal with this.
Directories are great, but don't write off the idea of getting onto google. I didn't think much about it, but I'd picked up a little SEO knowledge through years of being a big internet geek, so applied that to my site. This is less stuff than you'll find out in a quick chat with one of the SEO folks who float around the forums, but after a while I got to the top 10 in google for some good searches and I do get clients direct from google.