I've had lots of cloudy water problems in the past. I'm not sure what
fixed it though. I had an under gravel filter at one point, and I
think that helped it some what. Although I have removed it as my
loached kept finding their way under it and I could never find them!

About the waste buildup... I usually don't clean up waste that builds
up under anything, as I don't want to move around too much in the tank
when I clean it. I find I don't need to clean it up though. I have
corys and loaches in my tank, along with some other bottom feeders. I
think that these fish help with the waste problem. I think some large
snails would also take care of any waste laying around.

I also think that an underground filter would help get rid of the waste
because it will suck the waste into the bottom where it won't be
visible and will also help create beneficial bacteria that will help
keep the water clear.

Hope this helps!