It is a million times easier to clean the tanks if there is no gravel in the bottom. As debris gets trapped in their and can make your tank constantly dirty. I would recomend getting rid of it. There are also impaction risks.
If you do decide to keep the gravel then it should be stirred frequently to stir up the debris into the water column thereby allowing the filter to get some of it out.
Wether or not you keep the gravel you shuld do frequent partial water changes. It is never a good idea to do 100% water changes as this resets your nitrite cycle and that is bad news. Weekly or biweekly water changes of no more than 30% of the water are good. As your turtles get bigger and make more mess you may find yourself cleaning more often.
As far as the actual cleaning, by a water siphon or a Python. A water siphon is a tool for cleaning fish tanks, its a long tube attached to a bigger tube. Using gravity (pumping the larger tube up and down) it will suck water out and into a bucket. There are directions on the package that make it look much easier than it sounds...and it really is easy. The important thing is, if you keep your gravel, to make sure you put the siphon down into the gravel to suck up all the scum. A python is a larger more expensive form of the siphon that hooks to your sink. It works REALLY well, i have one for my 55gallon fish tank. YOu may want to do some reading on the nitrite cycle..also called the nitrogen cycle..whcih can be found in any book on aquarium fish, to understand how cleaning works and how to control algae etc..
As far as filters, canaster is the way to go, the Fluval canasters are pretty good.
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0.1 Bearded dragon
0.1 mexican Black kingsnake
1.1 Leopard Gecko's
0.0.1 Tokay Gecko
1.0 Blue Tongue Skink
0.0.1 Reverse Okeetee Corn
0.1 Anerythristic Corn
0.0.1 Red Tegu
0.1 Bullmastiff
4.1 Cats