Should I replace my cyclone/barrel style filter with something else or just remove it entirely?

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So here is a pic of my upper pond mostly empty (I'm refilling and pumping out again to get rid of more sludge).

The bottommost central portion is relatively flat, but there are multiple tiered/sloped portions.

Should I:

Put a (shortened or curved) bog outlet pipe only in the central portion (currently partially filled with water)? This section is maybe 4 feet across (left to right in the picture)

Or

Arrange the pipe so that a portion of it is laid along the shelf on the right? Note that the water level would still be about 4 inches above the pipe over there.

The bog pipe will be entering from the rear right, in the pic (just past where the hose currently is)
 

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E.g., I could curve that flexible pipe along the shelf that the hose is resting on, toward the camera, then at the end of the shelf 45 it down to the very bottom to feed a length of regular PVC (maybe a T that splits left and right in the pic)
 
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I would use standard rigid pvc pipe to accomodate the necessary slices which will allow the water to seep out. And I would place it in the deepest area. Just my two cents.
 
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Related question: any reason not to use the black flexible PVC for the bog pipe?
YOU'LL WANT TO USE PRESSURE FITTING WHEN USING FLEX PVC / THEY ARE STANDARD SCECHEDULE 40 BUT HAVE A DEEPER COLLAR TO SLIDE OVER THE PIPE
 
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yes and you'll want the pressure pvc coupling, there is nothing fancy about them they are no hard to find
 
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Got the piping done yesterday between rain showers and added just a bit of the pea gravel to get things leveled out and do some testing. Ugh, the pea gravel dirt
 
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Trying to follow the "pea gravel should be above the water level" guideline but obviously can't do that the closer I get to the waterfall to the lower pond. Any suggestions on how to handle this transition? My thought is to have a hollowed out area near that waterfall (as shown in the attached pics) but also hollow out an area below the upper falls so the water pools there a bit instead of flowing directly to and over the lower falls. Then I'll add sort of a pea gravel and bog plant dam between the two to force the water to go through it (of course being mindful that I don't disturb the flow so much that the water escapes the bog)
 

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Looks like that'd work - but because I've had a bog covered in water that became a thick mass of string algae, I'd try to minimize the amount of gravel underwater. Maybe create a rock barrier behind the pool so you can add a bit more gravel behind it. And then go plant shopping :)
 

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