Ahh see I'm not the only one that substrate is a PAIN, its almost TOO natural, have you smashed one between your fingers? it seems like a really nice soil of some sort, but if you move it around it stirs up stuff every single time grr its frustrating lol. I have found that when I move stuff around I simple turn the filter off let everything settle, then fire it back up to clear it up quickly, otherwise you will clog up the filter or it will take alot longer to clear.
On a side note how do you feel about the filter, did you adjust the flow down? I have that same filter in my 10 gallon and it can create a vortex in there can't imagine what its like in small space like the EBI. I tried turning the flow down and it got a little noisy, ended up drilling alot more holes in the spray bar.