I have the LCN correct in order just find out what is the difference from C=Control Channel or A=Alternate. If I didn't have LCN in order it would lock up on the Control Channel and I had to keep hitting scan 20 times to scan again.
If it's an EDACS system as mentioned above, the control channel designation (C or A) is irrelevant: you need
all of the frequencies.
For other (MOT and P25) systems, though, you should program anything that's listed as either "C" (primary control channel) or "A" (alternate control channel). This is so the scanner will continue to monitor the system in case the control channel rotates / changes to something other than the "primary". For example, my local system changes the control channel daily, cycling through all 4 listed C and A frequencies. If I didn't program them all, I'd only hear traffic every 4 days.