Two Days With a Two Year Old
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I, too, think you're absolutely right to spread this trip over two days. Your son will be just as happy playing in a small town playground as visiting the most spectacular natural attraction, so you might want to just look for some quieter places along the way, where all of you might enjoy some relaxing time out of the car. For my money, this describes many of the state parks you're going to be passing as you head down I-85 through North Carolina, including Kerr Lake State Recreation Area, Falls Lake State Park, and Crowders Mountain State Park.
Once in South Carolina, there is a great alternative to I-85, and that is the Cherokee Foothills Scenic Byway which basically follows SC-11 past Cowpens National Battlefield, Jones Gap State Park, Caesars Head State Park, Devils Fork State Park, and the only covered bridge in South Carolina. Near the end of the Scenic Byway, at Westminster, SC, take US-76, US-123, GA-115 and GA-17 into Helen. These would all be some of the 'back roads' that Tim mentioned.
Should be a great drive.
AZBuck