You're right, Jim. What you're doing is really really far from being the best method.
There are two ways in which you could get files from Motion to FCP with the original transparency intact. If you really want to work with Quicktime files, you can export from Motion a QT movie with the Animation codec (the only standard video codec that supports embedding tranparency along the usual color information). Don't worry, you don't need to go into the details yourself. When you export your Motion file, just pick in the Export window a preset called "lossless with alpha". This kind of file requires rendering in FCP, but it's really quick. Just a couple of seconds to transcode it to your sequence native codec.
The other (really cool) way of doing this is... not exporting anything! You see, Final Cut Pro has the ability to understand Motion projects as if they were video files! Just import your Motion project into FCP and drag it into the timeline. Yes, there will be some longer rendering required (because you're importing a RAW, unprocessed project file). The quality and the convenience are amazing, because if you select the clip, control-click and choose "Open in editor", you call Motion from FCP to quickly edit the text or any other thing you may need.
Sorry, I didn't understand what you mean when you talk about Motion behaviors and FCP wipes. Motion's behaviors are not transitions.
Hope this helps.
Adolfo Rozenfeld
Buenos Aires - Argentina
www.adolforozenfeld.com