WebAssist is actually in the process of making everything go into one folder. Universal Email 4 happened to be the first extension that was created under that new logic -- which is why you will also see your Digital File Pro stuff go under the webassist folder. The plan going forward, as I understand it, will continue to get everything to just use the webassist folder upon release.
Also, if you look at the planned roadmap for WebAssist's PHP Framwork and Includes, you will be able to organize your sites anyway you want upon release. It's probably the one extension I am most excited about and really look forward to.