i was having to make multiple watermarked copies of DVDs last year.
basic approach was to use TIFFs and add the watermark in Compressor (it;s in the "effects" section of the inspector)
at that time we didn't have PhotoShop, so i was actually creating the (simple!) watermarks in FCP.
i exported from FCP as TIFFs. these would behave properly as a watermark.
i since worked out that i could have used any format (the default PNG, say) and just asked for an alpha channel.
no biggie. same amount of clicks, and the watermark looked fine.
the watermarks were originally set to 50% opacity,
but we dropped them down to much less than that.
10% perhaps?
the great thing about Compressor is that i can have a number of pre-sets established.
i created pre-sets with whole clusters of people's watermarks.
i would NOT "export using Compressor" from FCP.
it ties up FCP for too long.
rather, i always export from FCP as self contained QTMovie,
then do my Compressor work in Compressor.
biggest drag was that the WM's were supposed to be dated,
so we had to create new ones quite often.
it wasn't hard to do it,
but it would be great if compressor had an auto-dating function in it's WM.
but as i said it wasn't too hard to make a new one, and overwrite the old one.
then Compressor would link directly to the new one.
nick