When multiple U.S. military aircraft are operating in formation, they do so as a "flight". This flight has a callsign, and in the case of Presidential transport flights, this callsign is the Presidential one, such as Air Force One or Marine One.
For POTUS transport using a fixed-wing aircraft, the flight typically consists of a single aircraft, usually one of the VC-25s specifically built for the purpose. Its fighter escort, if any (typically there is one), is a different "flight" that operates in tandem with Air Force One as the escort "element" of the complete transportation "package". Therefore, for Air Force One and for Navy or Executive fixed wing equivalents, the aircraft is the flight and has the callsign.
When the "Marine One" helicopters must be used, however, a very sophisticated "shell game" is played, as you already know. Not only are multiple helicopters used (I've seen up to 6 in use at the same time), they are externally identical in appearance, and they change position in the flight formation constantly. The Secret Service has even gone so far as to use body doubles that would make positive ID of the helicopter the actual President has entered difficult, even if an enemy faction had spotters in place to track each individual helicopter's position in the flight the whole time it's in the air.
This entire flight of multiple helicopters is what carries the "Marine One" callsign. Individual aircraft within the flight, if typical military radio procedures are followed, would be identified by adding a craft number suffix: "Marine One-One", "Marine One-Two", etc. I don't know whether the aircraft change craft numbers during flight to match formation position, or if the pilots just keep track of which chopper's where as they juggle.
So, a potential assassin would either have to take a 50-50 shot (or worse) at one of the choppers in the flight, or he'd have to coordinate with multiple launchers to attack all the choppers simultaneously (and the larger the effort, the more communication is required to plan and execute it, which increases the group's exposure and the potential for detection). If there is any reliable intel that the President would be targeted with this level of sophistication during a visit, he usually doesn't go; he has a VP, a Secretary of State and a cadre of ambassadorial representatives whose job it is to personally represent the President anywhere in the world the President himself cannot be, for any reason.