[eluser]BrianDHall[/eluser]
Actually, you'll be pleased to find that CI does not touch _COOKIE or _SESSION at all. CI's Sessions implementation doesn't touch or even effect PHP's native session system, so you don't have to do anything special to get your existing system working with CI.
The only thing CI clears is _GET.
So yeah, you should find that the only issue with your existing system is you don't get the additional ease of use provided by CI's built-in session implementation. Otherwise you are good to go.