Where do the small wires connect to?

Battery post on starter relay
Frame ground point

Universal (non Mopar) cables. you could run the neg one to the radiator support or any nearby ground. Likely no use for the red pigtail

Ok

I'd go ahead & run the large red cable to the starter relay large batt stud then a large cable from that stud down to the starter (std Mopar routing) and the black large cable to the block & the black pigtail to any nearby ground & in addition a good braided cable or regular cable from block to firewall

From the factory, the ground cable does not have a small pigtail wire. The factory positive cable large end attached to the stud on the starter. The smaller gauge wires feeds to the relay on the firewall. There is an additional wire from the relay down to small stud to starter (brown wire). Pull up a wire diagram form the year car and you can see how it should be wired.