First off: Downloaded material is most of the time a bad choice for editing. It often gets unstable, glitchy and the quality is not as good as dvd source. Also prework for the source can get more frustrating.
I suggest you buy the DVDs, read this guides:http://www.animemusicvideos.org/guides/avtech3/
and than you read this guide on how you can use your knowledge on a Mac:viewtopic.php?f=65&t=95075&start=0
I never used Flip4Mac, but there are some possibilites:
-You might be able to turn of the watermark in the preferences of Flip4Mac
-You might have to buy/donate to Flip4Mac to make it dissapear
Did you tried Perrian? It's something "similar" to Flip4Mac and is freeware. It shouldn't leave a watermark.http://perian.org/