OneCare will potentially detect the actions of a root kit in that a root kit is typically there to further infect your machine with malware. A root kit can only be surmised through a tricky comparison of the registry and memory.
Any real time protection will potentially cause conflicts, so I would recommend against installing any. You can use a program to scan for root kits as long as they are not always running. If you are not infected by a root kit at this point, it is not likely that you will be infected as OneCare (along with the Defender functionality in OneCare) will detect the actions of a root kit trying to install itself.