What does Miss Maudie mean by "sometimes the Bible in one hand of one man is worse than a whiskey bottle in the hand of-oh your father?"

Miss Maudie means that it is the person using a substance that matters, not the substance itself. The Bible, usually seen as a positive moral force, can become a force for evil in the wrong hands. Likewise, whiskey, often seen as evil force driving people to drunkenness, won't be as damaging if consumed by an ethical man like Atticus.
This points to Atticus as the moral center of the book. A good part of Scout's education during the novel is in her learning that her father is an exemplary human being, a man of character guided by conscience. Here we learn that we don't know what might go on behind closed doors at the Radleys, nor how their private behavior might differ from their public behavior. As Miss Maudie says:

"The things that happen to people we never really know. What happens in houses behind closed doors, what secrets—”

When Scout defends Atticus by saying he treats her and Jem the same way whether they are in the house or in the yard, Miss Maudie agrees. This consistency shows that Atticus is a man of integrity.

Miss Maudie means that the Bible can be harmful when someone uses its content for evil. Even though the Bible is meant to inspire hope and love in modern Christian theology, people can twist its words in a negative way and use it to justify negative actions. Alcohol, on the other hand, was often seen as a negative; but it is all about the person using it, Miss Maudie says.
Miss Maudie is explaining to Scout what she knows about the Radley family. Scout is curious about Arthur "Boo" Radley, a shut-in who Scout, Jem, and Dill wonder about all summer. Miss Maudie knew him as a child and explains that his family was very religious. They belonged to a type of Baptist group that Miss Maudie calls "foot-washing Baptists." They believed that every type of pleasure was sinful. 
Miss Maudie tells Scout:

"Wasn’t talking about your father," she said. "What I meant was, if Atticus Finch drank until he was drunk he wouldn’t be as hard as some men are at their best. There are just some kind of men who—who’re so busy worrying about the next world they’ve never learned to live in this one, and you can look down the street and see the results."

In this way, she is explaining how Boo Radley's father twisted the Bible's messages and made his home a sad one.