Using Windows Live Writer is great with BlogEngine.NET, in fact it's preferable for one specific reason: the included HTML editor in BlogEngine messes up your inline code.  If you're trying to use my flv player extension you may have noticed that even when you use the HTML view (not WYSIWYG) your code still gets formatted and the video won't display.  The trick is to use WLW but when you publish your post, make sure your view is HTML Code (Shift+F11).  Then your inline code won't be altered.

Setting up WLW is easy, just put the Weblog Homepage URL of your blog like the example below and WLW will autodetect everything else. That's all WLW needs.