But you are free to change it whenever you like. So set it to 5V, read pin 1. Set it to 2,5V, read pin 2.
The internal references are connected to the same pin as the external reference (AREF pin) so YOU CAN'T USE BOTH. The Arduino UNO only has the internal 5V and 1.1 (+/-.1) internal references. To use a 2.5V reference you would have to connect an external 2.5V source to the AREF pin. If you switch to the Internal 5V reference while an external reference is connected, the internal 5V source and your external 2.5V source would be connected together and fight each other.
Note: It might be possible to put a diode between the external source and the AREF pin so that the higher Internal voltage won't pass to the external source. You would need a slightly higher external source to compensate for the diode's voltage drop. This trick only works when the Internal source is a higher voltage than the External source.
If you use an Arduino MEGA 2560 you can switch between the internal 5V and internal 2.56V references.