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How long should i leave my Reptofilter on for?

Also, the waterfall makes some of the stuff get pushed away. Is there an easy way to stop this? I can put the filter so that there isnt a waterfall but would that affect the usefulness of the filter?

You should (and probably need to) leave your filter on 24 hours a day, it's usually only off when you clean it out, since turtles are very messy and can dirty up the water in minutes without proper filtration (skin shedding for example).

I'm not sure what you mean by "stuff get pushed away", what is this "stuff"?

But as for stopping the waterfall, no, it would not affect the usefulness of the filter, as long as the clean filtered water gets into the tank and doesn't come into contact with dirty unfiltered water from the tank, which would defeat the purpose of water filtration.

the stuff are things getting sucked up by the filter then getting pushed back away from the waterfall which is underwater.

So things in the process of being sucked towards the intake is disturbed and moved away by the waterfall?

Correct

Well under normal circumstances, that shouldn't happen, if you haven't cleaned out your filter and replaced the media lately, you can try doing so, it will improve the performance and the intake will be more powerful to take things in.

Otherwise, increase the water level or do whatever you think will work best for you to reduce the length of the waterfall, the higher the water falls, the harder stuff will be moved around.