There is only one signalling server, and both URLs (multiplayer.scirra.com and multiplayer.construct.net) point to the same server.
I'd recommend updating any existing projects to refer to multiplayer.construct.net. While we intend to keep the multiplayer.scirra.com URL alive for backwards compatibility purposes, we cannot guarantee it will continue to be running in the long term, as our long term goal is to move over everything to run on the construct.net domain.