One way to ensure that you cannot add a duplicate gift is to use a variation of the third party system's gift ID as the Raiser's Edge Gift ID.
To ensure that this modified Gift ID does not match an existing Raiser's Edge Gift ID, we recommend using a Data Transformation to add a prefix to the number. You can watch a video walk through of this process here (it features the EveryAction data source, but the princple may be used with any data source).
Please note that you should not change the prefix after you begin using this system or the contributions will no longer match and you may inadvertently duplicate gifts.