Hey, I have experience defintely with Flex, and did a little work in the past with IIS, but not at the same time unfortunately.

I'm not sure how much you know about Flex, but Flex is completely client side, and IIS is of course server side.  If not connecting your application to data, all you need for Flex is an HTTP server to dole out the files and HTML.  The user's browser will take care of the rest (just like a normal webpage with images).

Assuming you want to connect to data, though, there are a few options you can use.  You can of course make rest-based services, but you probably want something a little easier/quicker.  I've seen that IIS/Visual Studio has some great Soap service creators that are pretty automatic.  And Flex has some great tools to auto-discover attributes in your Soap service.

So if you need data connectivity, and are working with IIS, I'd recommend soap.   But there's really nothing different about working with IIS and Flex than say Apache/PHP and Flex, or anything else (unless it's coldfusion, that'll do all the work for you and make sandwiches I've heard)