The earmakrs aren't a part of the bill when it's voted on. they are added on as committee recs. later on- giving the President the option to ignore them
The earmarks are in the bill when the leaders of the respective houses sign it. Regardless of when they're negotiated, they don't go in after the final vote and signature.
The conference report consists of the amendments that the two house have agreed on in conference. They then go back to each house and are voted on. If agreed to they become law. Period.