When you are talking about one of the things being replaced, you use by - A is being replaced by B - A was replaced by B When you're talking about the thing that is doing the replacement, you use with - I will replace A with B - she replaced A with B

Replaced with is better in most situations. My best guess for now. I would just say replace with and you cant go wrong.

Depends on context, did you have an example in mind?