You can upload documents via the links window. So that's .doc, .pdf, .txt, etc. Select some text, click the Link tool, then choose to upload a file. Once you've done that, you can delete the link but the text file you uploaded will still be there.
As for directories, you can create directories as per usual but they aren't writable by default. If you need to create one, let me know and I'll make it writable. We're still working on a fix for that.
Finally, for SWFs which need to load files, you need to include a BASE param in your SWF embed. Because the article and the swf don't reside in the same directory, the Flash player goes looking for the loaded files in the same directory as the HTML file instead of the SWF file ( a stupid bug in the Flash player if you ask me). The solution is to include:
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,29,0" align="" height="363" width="500">
<param name="base" value="/resources/content_images/3/"/>
<param name="movie" value="/resources/content_images/3/date.swf"/>
<param name="src" value="/resources/content_images/3/date.swf"/>
<param name="play" value="true"/><param name="wmode" value="opaque"/>
<param name="scale" value=""/><param name="quality" value="high"/>
<param name="menu" value="true"/><param name="bgcolor" value=""/>
<embed base="/resources/content_images/3/" src="/resources/content_images/3/date.swf" scale="" wmode="opaque" play="true" quality="high" menu="true" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" width="500" height="363" align="" bgcolor=""/></object>
/resources/content_images/3/ in the above is where the SWF actually is, and thus, where the files you are trying to load also sit. 3 will have to be replaced with your own Author ID (which you see in the upload window, above the file list whenever you try to upload any kind of file).
Nasty hack I know. I'm going to see if we can edit the Flash insert mechanism to include this by default going forward. Should be possible, but for those tutorials already online, they'll need the manual edit.