Help you WITH English means to help you learn English.
Example: Can you help me with English ? It's a very difficult language.
Help you IN English means to speak English in order to help someone.
Example: If I am in a library in China, I would find an employee and say "Excuse me, Can you help me in English? I can't speak Chinese."
But like Danielle said, it's rather common to hear other ways of using those words.
For example: "I'm bad with numbers, so my friend is going to help me in math."
The full sentence would be "...my friend is going to help me in math CLASS." It means your friend is going to help you WITH math while you are both IN math class.
Hope I didn't confuse you any further :p