I have a Red Sea Prizm on my JBJ that worked out of the box without modding the tank or hood. The inlet pipe drops into the center section which places the output directly over the right hand return pump chamber (when looking at the front of the tank). I do not use a media basket, so there were no interference issues at all. If you use the media basket, you can trim the wide return ramp on the Prizm and put the input tube into the left return pump chamber and the output will drop into the center chamber. You only need to remove about 1/2" from the return ramp (right up to the set screw mounting point.) If you put it in this way, you'll have to remove the skimmer when you need to access your media basket.
It's not a "great" skimmer, but it works well enough and does not interfere with the lid operation at all.
Mac