Install a piece of sponge on the intake tube. So it is outside the filter. Yes, it will reduce the water flow.
You are supposed to remove all of the organic waste during the partial water change. Do a gravel vacuuming when you remove the water from your fish tank. If you do not remove them, they will just pile up and increase the ammonia production in your aquarium. Maybe your siphon does not have enough sucking power?
My gravel vacuum works just fine. It doesn't even remove the small piece of substrate since they will just fall back down right away.
