With a filter, you don't need to do 100% water changes that often. 50% once a week is fine, then you don't need to take him out. There's a link at the top of this forum by oldfishlady that is a great resource on water changes, how often and how much you should do.
Also, with that type of filter, you need to make sure the water is up to the lip of the flow, otherwise, the water flow in the tank will be too much for him. If it's right up to the lip of the filter, the surface water should be virtually still.
And as the previous poster stated, cleaning every inch of the tank is actually more harmful than good, because it can remove all the beneficial stuff that is helping your fish survive. When you remove all of it, your fish has to re-adapt to completely different water parameters, and that can be extremely stressful.