Hi ! Welcome to IRV2! We're sure glad you joined us!
I did the same swap-out a couple of years ago. I just matched the wires up color for color. You definitely want to stay with the new CCC2 thermostat if that's what you got. The flat phone cable is for communications between the thermostat and the rooftop units. I'm not positive, but I think the jacks for the phone cables are paralleled, so it won't make any difference which jack you use.
Good luck, happy trails, and God bless!
Joe & Annette
Sometimes I sits and thinks, sometimes I just sits.....
2002 Monaco Windsor 40PBT, 2013 Honda CRV AWD