as User 4869 said, Conan is talking about Haibara as you can tell he is looking at Professor Agasa's house while talking.
and about what Amuro meant, it can, as User 4869 said, means that he is talking about Conan's plan of faking Akai's death.
or
as what i can think is that he is talking about the "Sleeping Kogoro"?(unlikely)
well i can't say about what he actually meant by that?
i guess we have to wait until gosho aoyama tell us about it in file 898.