MacBeth... How does Malcolm become king?

They aren't related. Shakespeare believed that Banquo's son moved to Ireland; after a few decades, his son's sons returned to Scotland, became stewards to the Scottish king, and eventually became kings themselves.

This was the family history of James Stuart, the king of England when Shakespeare wrote the play. Thus, the scene when the witches show Macbeth the long line of kings is actually a tribute to King James.

Well, "future kings" doesn't have to mean "the next king after Macbeth." Some descendent of Banquo's will presumably be king someday.

As far as the witches go, it depends on what kind of take you have on them. Some people say that they actually control the actions of the characters in the play, some say they only prophesize (with Macbeth himself making the predictions come true), and some say they are like the three fates. Depending on your veiw of the witches, the answer to your question can vary a bit. Either they ensure that a descendent of Banquo's gets on the throne, or he tells his children (and children's children) about the prophesy and one of them fights his/her way to the throne.

Macbeth dishonored the throne and killed to achieve his ambition.