To 'clear something with somebody' means to inform them of something, so that they are in the clear, (are informed) and it usually involves getting their approval or at least acceptance. It is a phrase you would use with your boss or partner (husband/wife, friends). E.g. I like your suggestion, but I'll clear it my boss before I accept. To 'go' clear with him, is a phrase I've not heard. Depends on the context.

To clear it with someone means to get permission or agreement from someone