Yeah...some of the MW functions won't work if you don't use that product stuff (the first few icons in the toolbar). There are work-arounds for most of them though. Really the only thing MW does that you can't do in UG out of the box is offer you some handy component libraries and an interface that replaces a few manual mouse clicks. Almost everything else it does is stuff you can do manually and avoid all the MW overhead; wavelinks, trims, arrays, etc. The downside is, as mentioned, some of the misc functions won't work without that overhead existing in your assembly. It's getting better though....
Take care...