"Can the Align 35 Amp ESC be programmed with just the ESC plugged into the receiver?" Yes it can, but programming this wont help with setting up the servos. The esc only controls the motor and acts as a power source only for the servos. Someone here should be able to direct you to a manual for the ESC
what radio gear are you using? Was it setup at all when you bought it? The channels on the receiver should be labeled with stuff like RUD, AIL, ELE, etc. depending on your radio. The servos from your cyclic go in the ELE, AIL and AUX, but it might be different on your radio. You will just need to keep putting in one at a time until it moves in the right direction for both aileron and elevator controls.
For now i think you should keep the motor unplugged from the ESC to avoid accidental startup since this wont affect any of the other controls.