And in your rush to make the OP feel like an idiot, all of you missed the key part of his question.
Warft wants to know if setting up rxtools or reinand with an emunand will make him unable to use the existing save on his retail carts.
To answer your question, from what I understand if the save was created/played on a system with a firmware at 6.0 or higher, you will only be able to load the save on a system using 6.0 or higher. In the case of CFW like rxtools and reinand, as long as the emunand is at 6.0+ I THINK you are fine. Trying to extract the save to use with a .cia file might pose a problem or at least be complicated.
Btw, assuming he is talking about using the retail cart to play the game, he CAN use it with GW. He just has to load into Classic Mode instead of GW Mode.
Edit: This obviously only applies to games that use the 6.0+ save encryption. Older games do not have any issue at all.