Here's my story and fustration with the same prefilter box - I agree, the box wall and MJ1200 intake is too close and it's difficult to adjust. I'm on my 2nd week playing with it and I actually emailed Aqua C. To my surprise, I actually had a prompt response and cooresponded about 5 emails with them.
Basically, they said to adjust the box so that the water falls into the prefilter side of the box and aim the power heads towards the skimmer if possible as this will push the surface water towards the grooves .
- w/out the prefilter box - what did you use to cover the intake of the power head? My friend carved a little bit off the filter sponge and just popped it on the intake to prevent death by power head. I'm interested to hear what others are doing.