Did you list the three devices in the "Migration Devices" dialog box reached from the "Device" page of the "Settings" dialog box? When you tell Quartus to take care of the pin-by-pin differences between devices, the .pin and .fit.rpt files will tell you how to connect the pins in a way compatible with all devices you have selected for migration.
For pins 1, 2, and 3 being asked about here, Quartus tells you to connect them as FvM said: "The said pins must be connected to the respective supply voltages." From the .pin file in my test case:
Quartus II Version 8.0 Build 215 05/29/2008 SJ Full Version
CHIP "generic_test_case" ASSIGNED TO AN: EP3C10E144C7
Device Migration List: "EP3C16E144C7, EP3C25E144C7"
Pin Name/Usage : Location : Dir. : I/O Standard : Voltage : I/O Bank : User Assignment
-------------------------------------------------------------------------------------------------------------
VCCD_PLL3 : 1 : power : : 1.2V : :
GNDA : 2 : gnd : : : :
VCCA3 : 3 : power : : 2.5V : 1 :