I bet you have a JR / Spektrum radio. They have throttle on channel 1.
Deside what RC receiver protocol (PWM, PPM, SBus, DSM, etc.) you want to run and what your hardware supports. It may be that you have PPM in one place and PWM in the other place. PWM requires many cables from Rx to RC, one for each channel. PPM puts all the channels on one cable.
You could go to the Input -> RC Input page, with USB and flight battery connected and Tx on and wiggle the sticks one at a time and see whether you get activity showing (upper right corner).