Not necessarily. It will be separated by tags and descriptions in the same way FF8 PSX, FF8 PC, FF9, FF7 PSX, and FF7 PC already are. Not to mention that it looks like the new one could probably be made backwards compatible.
However, if you have a better idea for the layout, I'm all ears. Though it works better than what we used to have, I still get this feeling that the forums could be better/simpler...