We had the same issue in Lexington, and it really isn't a big problem. We split the registrations just as you are describing.
The only impact of one person with two cars that we could foresee would be if they wanted to enter both of them in the same activity, like the car show, or if another registered participant was going to drive the second one in a run that was concurrent with a run that the first car was in. Absent either of those situations, any number of cars wouldn't affect anything.
Sky NA 2007 Midnight Blue
Sky RL 2008 Carbon Flash - Naked