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This really depends on whether the two houses of Congress tend to agree with each other at a given time or not. For example, during the first two years of Pres. Obama's term, the House and Senate have not worked all that well together. The House leadership is much more liberal than the Senate and so that causes problems. This means that a lot of the time the two houses don't really work together.
Ideally, the House and Senate leadership can work together to make sure that they are passing (or at least considering) similar bills. So that is one way they can work together. If they do pass different versions of the same bill, they also work together in conference committee to get their versions to be identical. That is another way they work together.
Of course, both houses must pass a bill in identical form for it to become a law.
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