Yes. I believe I just made sure not to include the connection.js library from YUI. It wasn't necessary for the UI effects that I used. It and ASP.NET AJAX both trapping the XmlHttpRequest status changes is probably what would cause trouble using them together.
I've since moved on to mainly using jQuery for client side effects, so I'm not sure if more recent changes to YUI have made it harder to integrate. It should work fine though, as long as you're just using DOM effects.