Marshall
Turtle Keeper + CPL(H)
That is a common question and the short answer is I don't keep it clear. My bio-filter and UV-steralizer is the only intervention I use. My rules are if you have a bio-filter then keep substrate to a minimum. Trust me when I say the turtles do not give a 
whether the bottom has rocks or not. The more you add to the terrarium the more things you will have to scrub poop and debris off of. Rule number two is be patient. Don't expect any results for at least 3 days and even then expect minor ones. If it don't clear up by then you can then begin to tinker with the system. Also dont change the water everytime it gets just a little cloudy. The cloudiness is part of the normal cycle and it will take at the least 30 days for a bio-filter to truly be up and running and everytime you change the water or purge it you are resetting that cycle.
whether the bottom has rocks or not. The more you add to the terrarium the more things you will have to scrub poop and debris off of. Rule number two is be patient. Don't expect any results for at least 3 days and even then expect minor ones. If it don't clear up by then you can then begin to tinker with the system. Also dont change the water everytime it gets just a little cloudy. The cloudiness is part of the normal cycle and it will take at the least 30 days for a bio-filter to truly be up and running and everytime you change the water or purge it you are resetting that cycle.