They are obsolete pronouns and you may find them in religious texts today. They were used frequently in English literature.
I think, In Greek, you use one word to cover both you and thou: ΣΎ.
It means that you have one word in your language that covers two words in English, and that explains the difficulty.
About their exact usage, I have to say, structurally they had the same value and position as they have today. They just carry some literary value, and they were usually used to address familiar persons.
Here's an exceptional example; we expect your to be thine but it isn't. Maybe that's because of the structure.
So hence! Be thou the trumpet of our wrath
And sullen presage of your own decay.
Feel free to ask anything you find necessary.