Seems like whenever we flush whether is got number two, one, or is just flushed it doesn't seem to actually flush all the way down and fill properly what do we do?

There are several possible reasons for this issue. Lets start with an easy one, remove the tank lid and see if the water level is within an inch of the top of the small overflow tube. Back to you for your results. Have you tried plunging yet, I would give it a shot.

Check the connection between the handle and the flapper valve, if it's too loose shorten the chain until the valve will open all the way.

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doesn't seem to actually flush all the way down and fill properly what do we do?

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Explain how it "doesn't flush all the nway."
Does it fill to the top and swirl around and then slowly drain down? What doesn't "fill properly?" The tank? The bowl?
In shot we need more details.
Back to you, Tom