Does improper grounding cause resistance/heat?

My 2nd battery is decently grounded with 4gauge, but my front battery still has the dinky little stock ground.. My high output alternator powers both and I believe that the alt grounds itself through the car.. could the ground on the front battery cause the power traveling from the front to the back battery to make the wire get hot?? Is grounding probably my only problem??? I recently swapped the fuse to my sub amp to a 100amp ANL..