Alexandre,
Yes, this is possible (and easy) to do with APM.
There is one best practice to be aware of: AWS makes it simple to have non-distinct hostnames. e.g. Just start two instances from an AMI.
Because APM uses the "Host|Process|Agent" identifier to distinguish an agent's metrics, you want to make at least one of those unique per instance to avoid sending the same identifier from multiple AWS instances.
These can be provided as startup parameters to your agents, such as -DagentName as used in more recent versions.
Expect to see more information on running APM in AWS shortly, we're currently preparing some additional materials on it!